Alzheimer&#39;s disease secretase, APP substrates therefor, and uses therefor

ABSTRACT

The present invention provides the enzyme and enzymatic procedures for cleaving the β secretase cleavage site of the APP protein and associated nucleic acids, peptides, vectors, cells and cell isolates and assays. The invention further provides a modified APP protein and associated nucleic acids, peptides, vectors, cells, and cell isolates, and assays that are particularly useful for identifying candidate therapeutics for treatment or prevention of Alzheimer&#39;s disease.

[0001] The present application is a continuation of U.S. patentapplication Ser. No. 09/416,901, filed Oct. 13, 1999, which claimspriority benefit of U.S. Provisional Patent Application No. 60/155,493,filed Sep. 23, 1999; and which also claims priority benefit as acontinuation-in-part of U.S. patent application Ser. No. 09/404,133 andPCT/US99/20881, both filed Sep. 23, 1999, both of which in turn claimpriority benefit of U.S. Provisional Patent Application No. 60/101,594,filed Sep. 24, 1998. All of these priority applications are herebyincorporated by reference in their entirety.

FIELD OF THE INVENTION

[0002] The present invention relates to Alzheimer's Disease, amyloidprotein precursor, amyloid beta peptide, and human aspartyl proteases,as well as a method for the identification of agents that modulate theactivity of these polypeptides and thereby are candidates to modulatethe progression of Alzheimer's disease.

BACKGROUND OF THE INVENTION

[0003] Alzheimer's disease (AD) causes progressive dementia withconsequent formation of amyloid plaques, neurofibrillary tangles,gliosis and neuronal loss. The disease occurs in both genetic andsporadic forms whose clinical course and pathological features are quitesimilar. Three genes have been discovered to date which, when mutated,cause an autosomal dominant form of Alzheimer's disease. These encodethe amyloid protein precursor (APP) and two related proteins,presenilin-1 (PS1) and presenilin-2 (PS2), which, as their namessuggest, are structurally and functionally related. Mutations in any ofthe three proteins have been observed to enhance proteolytic processingof APP via an intracellular pathway that produces amyloid beta peptide(Aβ peptide, or sometimes here as Abeta), a 40-42 amino acid longpeptide that is the primary component of amyloid plaque in AD.

[0004] Dysregulation of intracellular pathways for proteolyticprocessing may be central to the pathophysiology of AD. In the case ofplaque formation, mutations in APP, PSI or PS2 consistently alter theproteolytic processing of APP so as to enhance formation of Aβ 1-42, aform of the Aβ peptide which seems to be particularly amyloidogenic, andthus very important in AD. Different forms of APP range in size from695-770 amino acids, localize to the cell surface, and have a singleC-terminal transmembrane domain. Examples of specific isotypes of APPwhich are currently known to exist in humans are the 695-amino acidpolypeptide described by Kang et. al. (1987), Nature 325: 733-736 whichis designated as the “normal” APP; the 751 amino acid polypeptidedescribed by Ponte et al (1988), Nature 331: 525-527 (1988) and Tanzi etal. (1988), Nature 331: 528-530; and the 770 amino acid polypeptidedescribed by Kitaguchi et. al. (1988), Nature 331: 530-532. The Abetapeptide is derived from a region of APP adjacent to and containing aportion of the transmembrane domain. Normally, processing of APP at theα-secretase site cleaves the midregion of the Aβ sequence adjacent tothe membrane and releases the soluble, extracellular domain of APP fromthe cell surface. This α-secretase APP processing creates soluble APP-α,which is normal and not thought to contribute to AD. Pathologicalprocessing of APP at the β- and γ-secretase sites, which are locatedN-terminal and C-terminal to the α-secretase site, respectively,produces a very different result than processing at the α site.Sequential processing at the β- and γ-secretase sites releases the Aβpeptide, a peptide possibly very important in AD pathogenesis.Processing at the β- and γ-secretase sites can occur in both theendoplasmic reticulum (in neurons) and in the endosomal/lysosomalpathway after reinternalization of cell surface APP (in all cells).Despite intense efforts, for 10 years or more, to identify the enzymesresponsible for processing APP at the β and γ sites, to produce the Aβpeptide, those proteases remained unknown until this disclosure.

SUMMARY OF THE INVENTION

[0005] Here, for the first time, we report the identification andcharacterization of the β secretase enzyme, termed Aspartyl Protease 2(Asp2). We disclose some known and some novel human aspartic proteasesthat can act as β-secretase proteases and, for the first time, weexplain the role these proteases have in AD. We describe regions in theproteases critical for their unique function and for the first timecharacterize their substrate. This is the first description of expressedisolated purified active protein of this type, assays that use theprotein, in addition to the identification and creation of useful celllines and inhibitors.

[0006] Here we disclose a number of variants of the Asp2 gene andpeptide.

[0007] In one aspect, the invention provides any isolated or purifiednucleic acid polynucleotide that codes for a protease capable ofcleaving the beta (β) secretase cleavage site of APP that contains twoor more sets of special nucleic acids, where the special nucleic acidsare separated by nucleic acids that code for about 100 to 300 amino acidpositions, where the amino acids in those positions may be any aminoacids, where the first set of special nucleic acids consists of thenucleic acids that code for the peptide DTG, where the first nucleicacid of the first special set of nucleic acids is the first specialnucleic acid, and where the second set of nucleic acids code for eitherthe peptide DSG or DTG, where the last nucleic acid of the second set ofnucleic acids is the last special nucleic acid, with the proviso thatthe nucleic acids disclosed in SEQ ID NO. 1 and SEQ ID NO. 3 are notincluded. In a preferred embodiment, the two sets of special nucleicacids are separated by nucleic acids that code for about 125 to 222amino acid positions, which may be any amino acids. In a highlypreferred embodiment, the two sets of special nucleic acids areseparated by nucleic acids that code for about 150 to 196, or 150-190,or 150 to 172 amino acid positions, which may be any amino acids. In aparticular preferred embodiment, the two sets are separated by nucleicacids that code for about 172 amino acid positions, which may be anyamino acids. An exemplary nucleic acid polynucleotide comprises the acidnucleotide sequence in SEQ ID NO. 5. In another particular preferredembodiment, the two sets are separated by nucleic acids that code forabout 196 amino acids. An exemplary polynucleotide comprises thenucleotide sequence in SEQ ID NO. 5. In another particular embodiment,the two sets of nucleotides are separated by nucleic acids that code forabout 190 amino acids. An exemplary polynucleotide comprises thenucleotide sequence in SEQ ID NO. 1. Preferably, the first nucleic acidof the first special set of amino acids, that is, the first specialnucleic acid, is operably linked to any codon where the nucleic acids ofthat codon codes for any peptide comprising from 1 to 10,000 amino acid(positions). In one variation, the first special nucleic acid isoperably linked to nucleic acid polymers that code for any peptideselected from the group consisting of: any reporter proteins or proteinswhich facilitate purification. For example, the first special nucleicacid is operably linked to nucleic acid polymers that code for anypeptide selected from the group consisting of: immunoglobin-heavy chain,maltose binding protein, glutathione S transferase, Green Fluorescentprotein, and ubiquitin. In another variation, the last nucleic acid ofthe second set of special amino acids, that is, the last special nucleicacid, is operably linked to nucleic acid polymers that code for anypeptide comprising any amino acids from 1 to 10,000 amino acids. Instill another variation, the last special nucleic acid is operablylinked to nucleic acid polymers that code for any peptide selected fromthe group consisting of: any reporter proteins or proteins whichfacilitate purification. For example, the last special nucleic acid isoperably linked to nucleic acid polymers that code for any peptideselected from the group consisting of: immunoglobin-heavy chain, maltosebinding protein, glutathione S transferase, Green Fluorescent protein,and ubiquitin.

[0008] In a related aspect, the invention provides any isolated orpurified nucleic acid polynucleotide that codes for a protease capableof cleaving the beta secretase cleavage site of APP that contains two ormore sets of special nucleic acids, where the special nucleic acids areseparated by nucleic acids that code for about 100 to 300 amino acidpositions, where the amino acids in those positions may be any aminoacids, where the first set of special nucleic acids consists of thenucleic acids that code for DTG, where the first nucleic acid of thefirst special set of nucleic acids is the first special nucleic acid,and where the second set of nucleic acids code for either DSG or DTG,where the last nucleic acid of the second set of special nucleic acidsis the last special nucleic acid, where the frrst special nucleic acidis operably linked to nucleic acids that code for any number of aminoacids from zero to 81 amino acids and where each of those codons maycode for any amino acid. In a preferred embodiment, the first specialnucleic acid is operably linked to nucleic acids that code for anynumber of from 64 to 77 amino acids where each codon may code for anyamino acid. In a particular embodiment, the first special nucleic acidis operably linked to nucleic acids that code for 71 amino acids. Forexample, the first special nucleic acid is operably linked to 71 aminoacids and where the first of those 71 amino acids is the amino acid T.In a preferred embodiment, the polynucleotide comprises a sequence thatis at least 95% identical to a human Asp1 or Asp2 sequence as taughtherein. In another preferred embodiment, the first special nucleic acidis operably linked to nucleic acids that code for any number of from 30to 54 amino acids, or 35 to 47 amino acids, or 40 to 54 amino acidswhere each codon may code for any amino acid. In a particularembodiment, the first special nucleic acid is operably linked to nucleicacids that code for 47 amino acids. For example, the first specialnucleic acid is operably linked to 47 codons where the first those 47amino acids is the amino acid E.

[0009] In another related aspect, the invention provides for anyisolated or purified nucleic acid polynucleotide that codes for aprotease capable of cleaving the beta (β) secretase cleavage site of APPand that contains two or more sets of special nucleic acids, where thespecial nucleic acids are separated by nucleic acids that code for about100 to 300 amino acid positions, where the amino acids in thosepositions may be any amino acids, where the first set of special nucleicacids consists of the nucleic acids that code for the peptide DTG, wherethe first nucleic acid of the first special set of amino acids is, thefirst special nucleic acid, and where the second set of special nucleicacids code for either the peptide DSG or DTG, where the last nucleicacid of the second set of special nucleic acids, the last specialnucleic acid, is operably linked to nucleic acids that code for anynumber of codons from 50 to 170 codons. In a preferred embodiment, thelast special nucleic acid is operably linked to nucleic acids comprisingfrom 100 to 170 codons. In a highly preferred embodiment, the lastspecial nucleic acid is operably linked to nucleic acids comprising from142 to 163 codons. In a particular embodiment, the last special nucleicacid is operably linked to nucleic acids comprising about 142 codons, orabout 163 codons, or about 170 codons. In a highly preferred embodiment,the polynucleotide comprises a sequence that is at least 95% identicalto aspartyl-protease encoding sequences taught herein. In one variation,the second set of special nucleic acids code for the peptide DSG. Inanother variation, the first set of nucleic acid polynucleotide isoperably linked to a peptide purification tag. For example, the nucleicacid polynucleotide is operably linked to a peptide purification tagwhich is six histidine. In still another variation, the first set ofspecial nucleic acids are on one polynucleotide and the second set ofspecial nucleic acids are on a second polynucleotide, where both firstand second polynucleotides have at lease 50 codons. In one embodiment ofthis type, both of the polynucleotides are in the same solution. In arelated aspect, the invention provides a vector which contains apolynucleotide as described above, or a cell or cell line which istransformed or transfected with a polynucleotide as described above orwith a vector containing such a polynucleotide.

[0010] In still another aspect, the invention provides an isolated orpurified peptide or protein comprising an amino acid polymer that is aprotease capable of cleaving the beta (β) secretase cleavage site of APPthat contains two or more sets of special amino acids, where the specialamino acids are separated by about 100 to 300 amino acid positions,where each amino acid position can be any amino acid, where the firstset of special amino acids consists of the peptide DTG, where the firstamino acid of the first special set of amino acids is, the first specialamino acid, where the second set of amino acids is selected from thepeptide comprising either DSG or DTG, where the last amino acid of thesecond set of special amino acids is the last special amino acid, withthe proviso that the proteases disclosed in SEQ ID NO. 2 and SEQ ID NO.4 are not included. In preferred embodiments, the two sets of aminoacids are separated by about 125 to 222 amino acid positions or about150 to 196 amino acids, or about 150-190 amino acids, or about 150 to172 amino acids, where in each position it may be any amino acid. In aparticular embodiment, the two sets of amino acids are separated byabout 172 amino acids. For example, the protease has the amino acidsequence described in SEQ ID NO 6. In another particular embodiment, thetwo sets of amino acids are separated by about 196 amino acids. Forexample, the two sets of amino acids are separated by the same aminoacid sequences that separate the same set of special amino acids in SEQID NO 4. In another particular embodiment, the two sets of nucleotidesare separated by about 190 amino acids. For example, the two sets ofnucleotides are separated by the same amino acid sequences that separatethe same set of special amino acids in SEQ ID NO 2. In one embodiment,the first amino acid of the first special set of amino acids, that is,the first special amino acid, is operably linked to any peptidecomprising from 1 to 10,000 amino acids. In another embodiment, thefirst special amino acid is operably linked to any peptide selected fromthe group consisting of: any reporter proteins or proteins whichfacilitate purification. In particular embodiments, the first specialamino acid is operably linked to any peptide selected from the groupconsisting of: immunoglobin-heavy chain, maltose binding protein,glutathione S transferase, Green Fluorescent protein, and ubiquitin. Instill another variation, the last amino acid of the second set ofspecial amino acids, that is, the last special amino acid, is operablylinked to any peptide comprising any amino acids from 1 to 10,000 aminoacids. By way of nonlimiting example, the last special amino acid isoperably linked any peptide selected from the group consisting of anyreporter proteins or proteins which facilitate purification. Inparticular embodiments, the last special amino acid is operably linkedto any peptide selected from the group consisting of: immunoglobin-heavychain, maltose binding protein, glutathione S transferase, GreenFluorescent protein, and ubiquitin.

[0011] In a related aspect, the invention provides any isolated orpurified peptide or protein comprising an amino acid polypeptide thatcodes for a protease capable of cleaving the beta secretase cleavagesite of APP that contains two or more sets of special amino acids, wherethe special amino acids are separated by about 100 to 300 amino acidpositions, where each amino acid in each position can be any amino acid,where the first set of special amino acids consists of the amino acidsDTG, where the first amino acid of the first special set of amino acidsis, the first special amino acid, D, and where the second set of aminoacids is either DSG or DTG, where the last amino acid of the second setof special amino acids is the last special amino acid, G, where thefirst special amino acid is operably linked to amino acids that code forany number of amino acids from zero to 81 amino acid positions where ineach position it may be any amino acid. In a preferred embodiment, thefirst special amino acid is operably linked to a peptide from about30-77 or about 64 to 77 amino acids positions where each amino acidposition may be any amino acid. In a particular embodiment, the firstspecial amino acid is operably linked to a peptide 35, 47, 71, or 77amino acids. In a very particular embodiment, the first special aminoacid is operably linked to 71 amino acids and the first of those 71amino acids is the amino acid T. For example, the polypeptide comprisesa sequence that is at least 95% identical to an aspartyl proteasesequence as described herein. In another embodiment, the first specialamino acid is operably linked to any number of from 40 to 54 amino acids(positions) where each amino acid position may be any amino acid. In aparticular embodiment, the first special amino acid is operably linkedto amino acids that code for a peptide of 47 amino acids. In a veryparticular embodiment, the first special amino acid is operably linkedto a 47 amino acid peptide where the first those 47 amino acids is theamino acid E. In another particular embodiment, the first special aminoacid is operably linked to the same corresponding peptides from SEQ IDNO. 3 that are 35, 47, 71, or 77 peptides in length, beginning countingwith the amino acids on the first special sequence, DTG, towards theN-terminal of SEQ ID NO. 3. In another particular embodiment, thepolypeptide comprises a sequence that is at least 95% identical to thesame corresponding amino acids in SEQ ID NO. 4, that is, identical tothat portion of the sequences in SEQ ID NO. 4, including all thesequences from both the first and or the second special nucleic acids,toward the − terminal, through and including 71, 47, 35 amino acidsbefore the first special amino acids. For example, the completepolypeptide comprises the peptide of 71 amino acids, where the first ofthe amino acid is T and the second is Q.

[0012] In still another related aspect, the invention provides anyisolated or purified amino acid polypeptide that is a protease capableof cleaving the beta (β) secretase cleavage site of APP that containstwo or more sets of special amino acids, where the special amino acidsare separated by about 100 to 300 amino acid positions, where each aminoacid in each position can be any amino acid, where the first set ofspecial amino acids consists of the amino acids that code for DTG, wherethe first amino acid of the first special set of amino acids is, thefirst special amino acid, D, and where the second set of amino acids areeither DSG or DTG, where the last amino acid of the second set ofspecial amino acids is the last special amino acid, G, which is operablylinked to any number of amino acids from 50 to 170 amino acids, whichmay be any amino acids. In preferred embodiments, the last special aminoacid is operably linked to a peptide of about 100 to 170 amino acids orabout 142-163 amino acids. In particular embodiments, the last specialamino acid is operably linked to a peptide of about 142 amino acids, orabout 163 amino acids, or about 170 amino acids. For example, thepolypeptide comprises a sequence that is at least 95% identical (andpreferably 100% identical) to an aspartyl protease sequence as describedherein. In one particular embodiment, the second set of special aminoacids is comprised of the peptide with the amino acid sequence DSG.Optionally, the amino acid polypeptide is operably linked to a peptidepurification tag, such as purification tag which is six histidine. Inone variation, the first set of special amino acids are on onepolypeptide and the second set of special amino acids are on a secondpolypeptide, where both first and second polypeptide have at lease 50amino acids, which may be any amino acids. In one embodiment of thistype, both of the polypeptides are in the same vessel. The inventionfurther includes a process of making any of the polynucleotides,vectors, or cells described herein; and a process of making any of thepolypeptides described herein.

[0013] In yet another related aspect, the invention provides a purifiedpolynucleotide comprising a nucleotide sequence that encodes apolypeptide having aspartyl protease activity, wherein the polypeptidehas an amino acid sequence characterized by: (a) a first tripeptidesequence DTG; (b) a second tripeptide sequence selected from the groupconsisting of DSG and DTG; and (c) about 100 to 300 amino acidsseparating the first and second tripeptide sequences, wherein thepolypeptide cleaves the beta secretase cleavage site of amyloid proteinprecursor. In one embodiment, the polypeptide comprises an amino-acidsequence depicted in SEQ ID NO: 2 or 4, whereas in another embodiment,the polypeptide comprises an amino acid sequence other than the aminoacid sequences set forth in SEQ ID NOs: 2 and 4. Similarly, theinvention provides a purified polynucleotide comprising a nucleotidesequence that encodes a polypeptide that cleaves the beta secretasecleavage site of amyloid protein precursor; wherein the polynucleotideincludes a strand that hybridizes to one or more of SEQ ID NOs: 3, 5,and 7 under the following hybridization conditions: hybridizationovernight at 42° C. for 2.5 hours in 6×SSC/0. 1% SDS, followed bywashing in 1.0×SSC at 65° C., 0.1% SDS. In one embodiment, thepolypeptide comprises an amino acid sequence depicted in SEQ ID NO: 2 or4, whereas in another embodiment, the polypeptide comprises an aminoacid sequence other than the amino acid sequences set forth in SEQ IDNOs: 2 and 4. Likewise, the invention provides a purified polypeptidehaving aspartyl protease activity, wherein the polypeptide is encoded bypolynucleotides as described in the preceding sentences. The inventionalso provides a vector or host cell comprising such polynucleotides, anda method of making the polypeptides using the vectors or host cells torecombinantly express the polypeptide.

[0014] In yet another aspect, the invention provides an isolated nucleicacid molecule comprising a polynucleotide, said polynucleotide encodinga Hu-Asp polypeptide and having a nucleotide sequence at least 95%identical to a sequence selected from the group consisting of:

[0015] (a) a nucleotide sequence encoding a Hu-Asp polypeptide selectedfrom the group consisting of Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b),wherein said Hu-Asp1, Hu-Asp2(a) and Hu-Asp2(b) polypeptides have thecomplete amino acid sequence of SEQ ID NO. 2, SEQ ID NO. 4, and SEQ IDNO. 6, respectively; and

[0016] (b) a nucleotide sequence complementary to the nucleotidesequence of (a).

[0017] Several species are particularly contemplated. For example, theinvention provides a nucleic acid and molecule wherein said Hu-Asppolypeptide is Hu-Asp1, and said polynucleotide molecule of 1 (a)comprises the nucleotide sequence of SEQ ID NO. 1; and a nucleic acidmolecule wherein said Hu-Asp polypeptide is Hu-Asp2(a), and saidpolynucleotide molecule of l(a) comprises the nucleotide sequence of SEQID NO. 4; and a nucleic acid molecule wherein said Hu-Asp polypeptide isHu-Asp2(b), and said polynucleotide molecule of l(a) comprises thenucleotide sequence of SEQ ID NO. 5. In addition to the foregoing, theinvention provides an isolated nucleic acid molecule comprisingpolynucleotide which hybridizes under stringent conditions to apolynucleotide having the nucleotide sequence in (a) or (b) as describedabove.

[0018] Additionally, the invention provides a vector comprising anucleic acid molecule as described in the preceding paragraph. In apreferred embodiment, the nucleic acid molecule is operably linked to apromoter for the expression of a Hu-Asp polypeptide. Individual vectorswhich encode Hu-Asp1, and Hu-Asp2(a), and Hu-Asp2(b) are allcontemplated. Likewise, the invention contemplates a host cellcomprising any of the foregoing vectors, as well as a method ofobtaining a Hu-Asp polypeptide comprising culturing such a host cell andisolating the Hu-Asp polypeptide. Host cells of the invention includebacterial cells, such as E. Coli, and eukaryotic cells. Among theeukaryotic cells that are contemplated are insect cells, such as sf9 orHigh 5 cells; and mammalian cells, such as human, rodent, lagomorph, andprimate. Preferred human cells include HEK293, and IMR-32 cells. Otherpreferred mammalian cells include COS-7, CHO-KL, Neuro-2A, and 3T3cells. Also among the eukaryotic cells that are contemplated are a yeastcell and an avian cell.

[0019] In a related aspect, the invention provides an isolated Hu-Asp 1polypeptide comprising an amino acid sequence at least 95% identical toa sequence comprising the amino acid sequence of SEQ ID NO. 2. Theinvention also provides an isolated Hu-Asp2(a) polypeptide comprising anamino acid sequence at least 95% identical to a sequence comprising theamino acid sequence of SEQ ID NO. 4. The invention also provides anisolated Hu-Asp2(a) polypeptide comprising an amino acid sequence atleast 95% identical to a sequence comprising the amino acid sequence ofSEQ ID NO. 8.

[0020] In still another aspect, the invention provides an isolatedantibody that binds specifically to any Hu-Asp polypeptide describedherein, especially the polypeptide described in the precedingparagraphs.

[0021] The invention also provides several assays involving aspartylprotease enzymes of the invention. For example, the invention provides amethod to identify a cell that can be used to screen for inhibitors of βsecretase activity comprising:

[0022] (a) identifying a cell that expresses a protease capable ofcleaving APP at the β secretase site, comprising:

[0023] i) collect the cells or the supernatant from the cells to beidentified

[0024] ii) measure the production of a critical peptide, where thecritical peptide is selected from the group consisting of either the APPC-terminal peptide or soluble APP,

[0025] iii) select the cells which produce the critical peptide.

[0026] In one variation, the cells are collected and the criticalpeptide is the APP C-terminal peptide created as a result of the βsecretase cleavage. In another variation, the supernatant is collectedand the critical peptide is soluble APP, where the soluble APP has aC-terminus created by β secretase cleavage. In preferred embodiments,the cells contain any of the nucleic acids or polypeptides describedabove and the cells are shown to cleave the β secretase site of anypeptide having the following peptide structure, P2, P1, P1′, P2′, whereP2 is K or N, where P1 is M or L, where P1′ is D, where P2′ is A. Themethod of claim 111 where P2 is K and P1 is M. The method of claim 112where P2 is N and P1 is L.

[0027] In still another aspect, the invention provides novel isoforms ofamyloid protein precursor (APP) where the last two carboxy terminusamino acids of that isoform are both lysine residues. In this context,the term “isoformm” is defined as any APP polypeptide, including APPvariants (including mutations), and APP fragments that exists in humans,such as those described in U.S. Pat. No. 5,766,846, col 7, lines 45-67,incorporated into this document by reference, modified as describedherein by the inclusion of two C-terminal lysine residues. For example,the invention provides a polypeptide comprising the isoform known asAPP695, modified to include two lysine residues as its last two carboxyterminus amino acids. An exemplary polypeptide comprises the amino acidsequence set forth in SEQ ID NO. 16. The invention further includes APPisoform variants as set forth in SEQ ID NOs. 18 and 20. The inventionfurther includes all polynucleotides that encode an APP protein that hasbeen modified to include two C-terminal lysines; as well has anyeukaryotic cell line comprising such nucleic acids or polypeptides.Preferred cell lines include a mammalian cell line (e.g., HEK293,Neuro2a).

[0028] Thus, in one embodiment, the invention provides a polypeptidecomprising the amino acid sequence of a mammalian amyloid proteinprecursor (APP) or fragment thereof containing an APP cleavage siterecognizable by a mammalian β-secretase, and further comprising twolysine residues at the carboxyl terminus of the amino acid sequence ofthe mammalian APP or APP fragment. As taught herein in detail, theaddition of two additional lysine residues to APP sequences has beenfound to greatly increase Aβ processing of the APP in APP processingassays. Thus, the di-lysine modified APP reagents of the invention areparticularly useful in assays to identify modulators of Aβ production,for use in designing therapeutics for the treatment or prevention ofAlzheimer's disease. In one embodiment, the polypeptide comprises thecomplete amino acid sequence of a mammalian amyloid protein precursor(APP), and further comprises the two lysine residues at the carboxylterminus of the amino acid sequence of the mammalian amyloid proteinprecursor. In an alternative embodiment, the polypeptide comprises onlya fragment of the APP, the fragment containing at least that portion ofAPP that is cleaved by a mammalian β-secretase in the formation of Aβpeptides.

[0029] The practice of assays that monitor cleavage of APP can befacilitated by attaching a marker to a portion of the APP. Measurment ofretained or liberated marker can be used to quantitate the amount of APPcleavage that occurs in the assay, e.g., in the presence or absence of aputative modulator of cleavage activity. Thus, in one preferredembodiment, the polypeptide of the invention further includes a marker.For example, the marker comprises a reporter protein amino acid sequenceattached to the APP amino acid sequence. Exemplary reporter proteinsinclude a fluorescing protein (e.g., green fluorescing proteins,luciferase) or an enzyme that is used to cleave a substrate to produce acolorimetric cleavage product. Also contemplated are tag sequences whichare commonly used as epitopes for quantitative immunoassays.

[0030] In a preferred embodiment, the di-lysine-modified APP of theinvention is a human APP. For example, human APP isoforms such asAPP695, APP751, and APP770, modified to include the two lysines, arecontemplated. In a preferred embodiment, the APP isoform comprises atleast one variation selected from the group consisting of a SwedishKM→NL mutation and a London V717-F mutation, or any other mutation thathas been observed in a subpopulation that is particularly prone todevelopment of Alzheimer's disease. These mutations are recognized asmutations that influence APP processing into Aβ. In a highly preferredembodiment, the APP protein or fragment thereof comprises the APP-Swβ-secretase peptide sequence NLDA (SEQ ID NO: 66), which is associatedwith increased levels of Aβ processing and therefore is particularlyuseful in assays relating to Alzheimer's research. More particularly,the APP protein or fragment thereof preferably comprises the APP-Swβ-secretase peptide sequence SEVNLDAEFR (SEQ ID NO: 63).

[0031] In one preferred embodiment, the APP protein or fragment thereoffurther includes an APP transmembrane domain carboxy-terminal to theAPP-Sw β-secretase peptide sequence. Polypeptides that include the TMdomain are particularly useful in cell-based APP processing assays. Incontrast, embodiments lacking the TM domain are useful in cell-freeassays of APP processing.

[0032] In addition to working with APP from humans and various animalmodels, researchers in the field of Alzheimer's also have constructchimeric APP polypeptides which include stretches of amino acids fromAPP of one species (e.g., humans) fused to streches of APP from one ormore other species (e.g., rodent). Thus, in another embodiment of thepolypeptide of the invention, the APP protein or fragment thereofcomprises a chimeric APP, the chimeric APP including partial APP aminoacid sequences from at least two species. A chimeric APP that includesamino acid sequence of a human APP and a rodent APP is particularlycontemplated.

[0033] In a related aspect, the invention provides a polynucleotidecomprising a nucleotide sequence that encodes a polypeptide as describedin the preceding paragraphs. Such a polynucleotide is useful forrecominant expression of the polypeptide of the invention for use in APPprocessing assays. In addition, the polynucleotide is useful fortransforming into cells to produce recombinant cells that express thepolypeptide of the invention, which cells are useful in cell-basedassays to identify modulators of APP processing. Thus, in addition topolynucleotides, the invention provides a vector comprising suchpolynucleotides, especially expression vectors where the polynucleotideis operably linked to a promoter to promote expression of thepolypeptide encoded by the polynucleotide in a host cell. The inventionfurther provides a host cell transformed or transfected with apolynucleotide according to claim 14 or a vector according to claim 15or 16. Among the preferred host cells are mammalian cells, especiallyhuman cells.

[0034] In another, related embodiment, the invention provides apolypeptide useful for assaying for modulators of β-secretase activity,said polypeptide comprising an amino acid sequence of the formulaNH₂—X—Y—Z—KK—COOH; wherein X, Y, and Z each comprise an amino acidsequence of at least one amino acid; wherein-NH₂—X comprises anamino-terminal amino acid sequence having at least one amino acidresidue; wherein Y comprises an amino acid sequence of a β-secretaserecognition site of a mammalian amyloid protein precursor (APP); andwherein Z—KK—COOH comprises a carboxy-terminal amino acid sequenceending in two lysine (K) residues. In one preferred variation, thecarboxyl-terminal amino acid sequence Z includes a hyrdrophobic domainthat is a transmembrane domain in host cells that express thepolypeptide. Host cells that express such a polypeptide are particularlyuseful in assays described herein for identifying modulators of APPprocessing. In another preferred variation, the amino-terminal aminoacid sequence X includes an amino acid sequence of a reporter or markerprotein, as described above. In still another preferred variation, theβ-secretase recognition site Y comprises the human APP-Sw β-secretasepeptide sequence NLDA (SEQ ID NO: 66). It will be apparent that thesepreferred variations are not mutually exclusive of each other—they maybe combined in a single polypeptide. The invention further provides apolynucleotide comprising a nucleotide sequence that encodes suchpolypeptides, vectors which comprise such polynucleotides, and hostcells which comprises such vectors, polynucleotides, and/orpolypeptides.

[0035] In yet another aspect, the invention provides a method foridentifying inhibitors of an enzyme that cleaves the beta secretasecleavable site of APP comprising:

[0036] a) culturing cells in a culture medium under conditions in whichthe enzyme causes processing of APP and release of amyloid beta-peptideinto the medium and causes the accumulation of CTF99 fragments of APP incell lysates,

[0037] b) exposing the cultured cells to a test compound; andspecifically determining whether the test compound inhibits the functionof the enzyme by measuring the amount of amyloid beta-peptide releasedinto the medium and/or the amount of CTF99 fragments of APP in celllysates;

[0038] c) identifying test compounds diminishing the amount of solubleamyloid beta peptide present in the culture medium and diminution ofCTF99 fragments of APP in cell lysates as Asp2 inhibitors. In preferredembodiments, the cultured cells are a human, rodent or insect cell line.It is also preferred that the human or rodent cell line exhibits βsecretase activity in which processing of APP occurs with release ofamyloid beta-peptide into the culture medium and accumulation of CTF99in cell lysates. Among the contemplated test compounds are antisenseoligomers directed against the enzyme that exhibits , secretaseactivity, which oligomers reduce release of soluble amyloid beta-peptideinto the culture medium and accumulation of CTF99 in cell lysates.

[0039] In yet another aspect, the invention provides a method for theidentification of an agent that decreases the activity of a Hu-Asppolypeptide selected from the group consisting of Hu-Asp1, Hu-Asp2(a),and Hu-Asp2(b), the method comprising:

[0040] a) determining the activity of said Hu-Asp polypeptide in thepresence of a test agent and in the absence of a test agent; and

[0041] b) comparing the activity of said Hu-Asp polypeptide determinedin the presence of said test agent to the-activity of said Hu-Asppolypeptide determined in the absence of said test agent; whereby alower level of activity in the presence of said test agent than in theabsence of said test agent indicates that said test agent has decreasedthe activity of said Hu-Asp polypeptide.

[0042] In a related aspect, the invention provides a method for assayingfor modulators of β-secretase activity, comprising the steps of:

[0043] (a) contacting a first composition with a second composition bothin the presence and in the absence of a putative modulator compound,wherein the first composition comprises a mammalian β-secretasepolypeptide or biologically active fragment thereof, and wherein thesecond composition comprises a substrate polypeptide having an aminoacid sequence comprising a p-secretase cleavage site;

[0044] (b) measuring cleavage of the substrate polypeptide in thepresence and in the absence of the putative modulator compound; and (c)identifying modulators of β-secretase activity from a difference incleavage in the presence versus in the absence of the putative modulatorcompound. A modulator that is a p-secretase antagonist (inhibitor)reduces such cleavage, whereas a modulator that is a β-secretase agonistincreases such cleavage. Since such assays are relevant to developmentof Alzheimer's disease therapeutics for humans, it will be readilyapparent that, in one preferred embodiment, the first compositioncomprises a purified human Asp2 polypeptide. In one variation, the firstcomposition comprises a soluble fragment of a human Asp2 polypeptidethat retains Asp2 β-secretase activity. Several such fragments(including ATM fragments) are described herein in detail. Thus, in aparticular embodiment, the soluble fragment is a fragment lacking anAsp2 transmembrane domain.

[0045] The β-secretase cleavage site in APP is known, and it will beappreciated that the oassays of the invention can be performed witheither intact APP or fragments or analogs of APP that retain theβ-secretase recognition and cleavage site. Thus, in one variation, thesubstrate polypeptide of the second composition comprises the amino acidsequence SEVNLDAEFR (SEQ ID NO: 63), which includes the β-secretaserecognition site of human APP that contains the “Swiss” mutation. Inanother variation, the substrate polypeptide of the second compositioncomprises the amino acid sequence EVKMDAEF (SEQ ID NO: 67). In anothervariation, the second composition comprises a polypeptide having anamino acid sequence of a human amyloid precursor protein (APP). Forexample, the human amyloid precursor protein is selected from the groupconsisting of: APP695, APP751, and APP770. Preferably, the human amyloidprecursor protein (irrespective of isoform selected) includes at leaston mutation selected from a KM→NL Swiss mutation and a V→F Londonmutation. As explained elsewhere, one preferred embodiment involves avariation wherein the polypeptide having an amino acid sequence of ahuman APP further comprises an amino acid sequence comprising a markersequence attached amino-terminal to the amino acid sequence of the humanamyloid precursor protein. Preferably, the polypeptide having an aminoacid sequence of a human APP further comprises two lysine residuesattached to the carboxyl terminus of the amino acid sequence of thehuman APP. The assays can be performed in a cell free setting, usingcell-free enzyme and cell-free substrate, or can be performed in acell-based assay wherein the second composition comprises a eukaryoticcell that expresses amyloid precursor protein (APP) or a fragmentthereof containing a β-secretase cleavage site. Preferably, the APPexpressed by the host cell is an APP variant that includes twocarboxyl-terminal lysine residues. It will also be appreciated that theβ-secretase enzyme can be an enzyme that is expressed on the surface ofthe same cells.

[0046] The present invention provides isolated nucleic acid moleculescomprising a polynucleotide that codes for a polypeptide selected fromthe group consisting of human aspartyl proteases. In particular, humanaspartyl protease 1 (Hu-Asp1) and two alternative splice variants ofhuman aspartyl protease-2 (Hu-Asp2), a “long” (L) form designated hereinas Hu-Asp2(a) and a “short” (S) form designated Hu-Asp2(b). As usedherein, all references to “Hu-Asp” should be understood to refer to allof Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b). In addition, as used herein, allreferences to “Hu-Asp2” should be understood to refer to both Hu-Asp2(a)and Hu-Asp2(b). Hu-Asp1 is expressed most abundantly in pancreas andprostate tissues, while Hu-Asp2(a) and Hu-Asp2(b) are expressed mostabundantly in pancreas and brain tissues. The invention also providesisolated Hu-Asp 1, Hu-Asp2(a), and Hu-Asp2(b) polypeptides, as well asfragments thereof which exhibit aspartyl protease activity.

[0047] In a preferred embodiment, the nucleic acid molecules comprise apolynucleotide having a nucleotide sequence selected from the groupconsisting of residues 1-1554 of SEQ ID NO. 1, encoding Hu-Asp1,residues 1-1503 of SEQ ID NO. 3, encoding Hu-Asp2(a), and residues1-1428 of SEQ ID NO.5, encoding Hu-Asp2(b). In another aspect, theinvention provides an isolated nucleic acid molecule comprising apolynucleotide which hybridizes under stringent conditions to apolynucleotide encoding Hu-Asp1, Hu-Asp2(a), Hu-Asp-2(b), or fragmentsthereof. European patent application EP 0 848 062 discloses apolypeptide referred to as “Asp 1,” that bears substantial homology toHu-Asp1, while international application WO 98/22597 discloses a V;polypeptide referred to as “Asp 2,” that bears substantial homology toHu-Asp2(a).

[0048] The present invention also provides vectors comprising theisolated nucleic acid molecules of the invention, host cells into whichsuch vectors have been introduced, and recombinant methods of obtaininga Hu-Asp1, Hu-Asp2(a), or Hu-Asp2(b) polypeptide comprising culturingthe above-described host cell and isolating the relevant polypeptide.

[0049] In another aspect, the invention provides isolated Hu-Asp1,Hu-Asp2(a), and Hu-Asp2(b) polypeptides, as well as fragments thereof.In a preferred embodiment, the Hu-Asp 1, Hu-Asp2(a), and Hu-Asp2(b)polypeptides have the amino acid sequence given in SEQ ID NO. 2, SEQ IDNO. 4, or SEQ ID NO.6, respectively. The present invention alsodescribes active forms of Hu-Asp2, methods for preparing such activeforms, methods for preparing soluble forms, methods for measuringHu-Asp2 activity, and substrates for Hu-Asp2 cleavage. The inventionalso describes antisense oligomers targeting the Hu-Asp1, Hu-Asp2(a) andHu-Asp2(b) mRNA transcripts and the use of such antisense reagents todecrease such MRNA and consequently the production of the correspondingpolypeptide. Isolated antibodies, both polyclonal and monoclonal, thatbinds specifically to any of the Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b)polypeptides of the invention are also provided.

[0050] The invention also provides a method for the identification of anagent that modulates the activity of any of Hu-Asp-1, Hu-Asp2(a), andHu-Asp2(b). The inventions describes methods to test such agents incell-free assays to which Hu-Asp2 polypeptide is added, as well asmethods to test such agents in human or other mammalian cells in whichHu-Asp2 is present.

[0051] Additional features and variations of the invention will beapparent to those skilled in the art from the entirety of thisapplication, including the drawing and detailed description, and allsuch features are intended as aspects of the invention. Likewise,features of the invention described herein can be re-combined intoadditional embodiments that are also intended as aspects of theinvention, irrespective of whether the combination of features isspecifically mentioned above as an aspect or embodiment of theinvention. Also, only such limitations which are described herein ascritical to the invention should be viewed as such; variations of theinvention lacking limitations which have not been described herein ascritical are intended as aspects of the invention.

[0052] In addition to the foregoing, the invention includes, as anadditional aspect, all embodiments of the invention narrower in scope inany way than the variations specifically mentioned above. Although theapplicant(s) invented the full scope of the claims appended hereto, theclaims appended hereto are not intended to encompass within their scopethe prior art work of others. Therefore, in the event that statutoryprior art within the scope of a claim is brought to the attention of theapplicants by a Patent Office or other entity or individual, theapplicant(s) reserve the right to exercise amendment rights underapplicable patent laws to redefine the subject matter of such a claim tospecifically exclude such statutory prior art or obvious variations ofstatutory prior art from the scope of such a claim. Variations of theinvention defined by such amended claims also are intended as aspects ofthe invention.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING

[0053] Sequence ID No. 1: Human Asp-1, nucleotide sequence.

[0054] Sequence ID No. 2: Human Asp-1, predicted amino acid sequence.

[0055] Sequence ID No. 3: Human Asp-2(a), nucleotide sequence.

[0056] Sequence ID No. 4: Human Asp-2(a), predicted amino acid sequence.The Asp2(a) amino acid sequence includes a putative signal peptidecomprising residues 1 to 21; and a putative pre-propeptide after thesignal peptide that extends through residue 45 (as assessed byprocessing observed of recombinant Asp2(a) in CHO cells), and a putativepropeptide that may extend to at least about residue 57, based on theobservation of an observed GRR↓GS (SEQ ID NO: 68) sequence which hascharacteristics of a protease recognition sequence. The Asp2(a) furtherincludes a transmembrane domain comprising residues 455-477, acytoplasmic domain comprising residues 478-501, and a putativealpha-helical spacer region, comprising residues 420-454, believed to beunnecessary for proteolytic activity, between the protease catalyticdomain and the transmembrane domain.

[0057] Sequence ID No. 5: Human Asp-2(b), nucleotide sequence.

[0058] Sequence ID No. 6: Human Asp-2(b), predicted amino acid sequence.The Asp2(b) amino acid sequence includes a putative signal peptide,pre-propeptide, and propeptide as described above for Asp2(a). TheAsp2(b) further includes a transmembrane domain comprising residues430-452, a cytoplasmic domain comprising residues 453-476, and aputative alpha-helical spacer region, comprising residues 395-429,believed to be unnecessary for proteolytic activity, between theprotease catalytic domain and the transmembrane domain.

[0059] Sequence ID No. 7: Murine Asp-2(a), nucleotide sequence.

[0060] Sequence ID No. 8: Murine Asp-2(a), predicted amino acidsequence. The proteolytic processing of murine Asp2(a) is believed to beanalogous to the processing described above for human Asp2(a). Inaddition, a variant lacking amino acid residues 190-214 of SEQ ID NO: 8is specifically contemplated as a murine Asp2(b) polypeptide.

[0061] Sequence ID No. 9: Human APP695, nucleotide sequence.

[0062] Sequence ID No.10: Human APP695, predicted amino acid sequence.

[0063] Sequence ID No.11: Human APP695-Sw, nucleotide sequence.

[0064] Sequence ID No.12: Human APP695-Sw. predicted amino acidsequence. In the APP695 isoform, the Sw mutation is characterized by aKM→NL alteration at positions 595-596 (compared to normal APP695).

[0065] Sequence ID No.13: Human APP695-VF, nucleotide sequence.

[0066] Sequence ID No.14: Human APP695-VF, predicted amino acidsequence. In the APP 695 isoform, the VF mutation is characterized by aV→F alteration at position 642 (compared to normal APP 695).

[0067] Sequence ID No.15: Human APP695-KK, nucleotide sequence.

[0068] Sequence ID No.16: Human APP695-KK, predicted amino acidsequence. (APP695 with two carboxy-terminal lysine residues.)

[0069] Sequence ID No.17: Human APP695-Sw-KK, nucleotide sequence.

[0070] Sequence ID No.18: Human APP695-Sw-KK, predicted amino acidsequence

[0071] Sequence ID No.19: Human APP695-VF-KK, nucleotide sequence

[0072] Sequence ID No.20: Human APP695-VF-KK, predicted amino acidsequence

[0073] Sequence ID No.21: T7-Human-pro-Asp-2(a)ΔTM, nucleotide sequence

[0074] Sequence ID No.22: T7-Human-pro-Asp-2(a)ΔTM, amino acid sequence

[0075] Sequence ID No.23: T7-Caspase-Human-pro-Asp-2(a)ΔTM, nucleotidesequence

[0076] Sequence ID No.24: T7-Caspase-Human-pro-Asp-2(a)ΔTM, amino acidsequence

[0077] Sequence ID No.25: Human-pro-Asp-2(a)ΔTM (low GC), nucleotidesequence

[0078] Sequence ID No.26: Human-pro-Asp-2(a)ΔTM, (low GC), amino acidsequence

[0079] Sequence ID No.27: T7-Caspase-Caspase 8cleavage-Human-pro-Asp-2(a)ΔTM, nucleotide sequence

[0080] Sequence ID No.28: T7-Caspase-Caspase 8cleavage-Human-pro-Asp-2(a)ΔTM, amino acid sequence

[0081] Sequence ID No.29: Human Asp-2(a)ΔTM, nucleotide sequence

[0082] Sequence ID No.30: Human Asp-2(a)ΔTM, amino acid sequence

[0083] Sequence ID No.31: Human Asp-2(a)ΔTM(His)₆, nucleotide sequence

[0084] Sequence ID No. 32: Human Asp-2(a)ΔTM(His)₆, amino acid sequence

[0085] Sequence ID Nos. 33-49 are short synthetic peptide andoligonucleotide sequences that are described below in the DetailedDescription of the Invention.

[0086] Sequence ID No. 50: Human Asp2(b)ATM polynucleotide sequence.

[0087] Sequence ID No. 51: Human Asp2(b)ATM polypeptide sequence(exemplary variant of Human Asp2(b) lacking transmembrane andintracellular domains of Hu-Asp2(b) set forth in SEQ ID NO: 6.

[0088] Sequence ID No. 52: Human Asp2(b)ATM(His)₆ polynucleotidesequence.

[0089] Sequence ID No. 53: Human Asp2(b)ATM(His)₆ polypeptide sequence(Human Asp2(b)ATM with six histidine tag attached to C-terminus)

[0090] Sequence ID No. 54: Human APP770-encoding polynucleotidesequence.

[0091] Sequence ID No. 55: Human APP770 polypeptide sequence. Tointroduce the KM→NL Swedish mutation, residues KM at positions 670-71are changed to NL. To introduce the V→F London mutation, the V residueat position 717 is changed to F.

[0092] Sequence ID No. 56: Human APP751 encoding polynucleotidesequence.

[0093] Sequence ID No. 57: Human APP751 polypeptide sequence (HumanAPP751 isoform).

[0094] Sequence ID No. 58: Human APP770-KK encoding polynucleotidesequence.

[0095] Sequence ID No.59: Human APP770-KK polypeptide sequence. (HumanAPP770 isoform to which two C-terminal lysines have been added).

[0096] Sequence ID No. 60: Human APP751-KK encoding polynucleotidesequence.

[0097] Sequence ID No. 61: Human APP751-KK polypeptide sequence (HumanAPP751 isoform to which two C-terminal lysines have been added).

[0098] Sequence ID No. 62-65: Various short peptide sequences describedin detail in detailed description.

BRIEF DESCRIPTION OF THE FIGURES

[0099]FIG. 1: FIG. 1 shows the nucleotide (SEQ ID NO: 1) and predictedamino acid sequence (SEQ ID NO: 2) of human Asp1.

[0100]FIG. 2: FIG. 2 shows the nucleotide (SEQ ID NO: 3) and predictedamino acid sequence (SEQ ID NO: 4) of human Asp2(a).

[0101]FIG. 3: FIG. 3 shows the nucleotide (SEQ ID NO: 5) and predictedamino acid sequence (SEQ ID NO: 6) of human Asp2(b). The predictedtransmembrane domain of Hu-Asp2(b) is enclosed in brackets.

[0102]FIG. 4: FIG. 4 shows the nucleotide (SEQ ID No. 7) and predictedamino acid sequence (SEQ ID No. 8) of murine Asp2(a)

[0103]FIG. 5: FIG. 5 shows the BestFit alignment of the predicted aminoacid sequences of Hu-Asp2(a) (SEQ ID NO: 4) and murine Asp2(a) (SEQ IDNO: 8).

[0104]FIG. 6: FIG. 6 shows the nucleotide (SEQ ID No. 21) and predictedamino acid sequence (SEQ ID No. 22) of T7-Human-pro-Asp-2(a)ΔTM

[0105]FIG. 7: FIG. 7 shows the nucleotide (SEQ ID No. 23) and predictedamino acid sequence (SEQ ID No. 24) of T7-caspase-Human-pro-Asp-2(a)ΔTM

[0106]FIG. 8: FIG. 8 shows the nucleotide (SEQ ID No. 25) and predictedamino acid sequence (SEQ ID No. 26) of Human-pro-Asp-2(a)ΔTM (low GC)

[0107]FIG. 9: Western blot showing reduction of CTF99 production byHEK125.3 cells transfected with antisense oligomers targeting theHu-Asp2 mRNA.

[0108]FIG. 10: Western blot showing increase in CTF99 production inmouse Neuro-2a cells cotransfected with APP-KK with and without Hu-Asp2only in those cells cotransfected with Hu-Asp2. A further increase inCTF99 production is seen in cells cotransfected with APP-Sw-KK with andwithout Hu-Asp2 only in those cells cotransfected with Hu-Asp2

[0109]FIG. 11: FIG. 11 shows the predicted amino acid sequence (SEQ IDNo. 30) of Human-Asp2(a)ΔTM

[0110]FIG. 12: FIG. 11 shows the predicted amino acid sequence (SEQ IDNo. 30) of Human-Asp2(a)ΔTM(His)₆

DETAILED DESCRIPTION OF THE INVENTION

[0111] A few definitions used in this invention follow, most definitionsto be used are those that would be used by one ordinarily skilled in theart.

[0112] The term “β amyloid peptide” means any peptide resulting frombeta secretase cleavage of APP. This includes peptides of 39, 40,41, 42and 43 amino acids, extending from the β-secretase cleavage site to39,40,41,42 and 43 amino acids C-terminal to the β-secretase cleavagesite. β amyloid peptide also includes sequences 1-6, SEQ ID NOs. 1-6 ofU.S. Pat. No. 5,750,349, issued May 12, 1998 (incorporated into thisdocument by reference). A β-secretase cleavage fragment disclosed hereis called CTF-99, which extends from β-secretase cleavage site to thecarboxy terminus of APP.

[0113] When an isoform of APP is discussed then what is meant is any APPpolypeptide, including APP variants (including mutations), and APPfragments that exists in humans such as those described in U.S. Pat. No.5,766,846, col 7, lines 45-67, incorporated into this document byreference.

[0114] The term “β-amyloid precursor protein” (APP) as used herein isdefined as a polypeptide that is encoded by a gene of the same namelocalized in humans on the long arm of chromosome 21 and that includes“βAP—here “β-amyloid protein” see above, within its carboxyl third. APPis a glycosylated, single-membrane spanning protein expressed in a widevariety of cells in many mammalian tissues. Examples of specificisotypes of APP which are currently known to exist in humans are the 695amino acid polypeptide described by Kang et. al. (1987) Nature325:733-736 which is designated as the “normal” APP (SEQ ID NOs: 9-10);the 751 amino acid polypeptide described by Ponte et al. (1988) Nature331:525-527 (1988) and Tanzi et al. (1988) Nature 331:528-530 (SEQ IDNOs: 56-57); and the 770-amino acid polypeptide described by Kitaguchiet. al. (1988) Nature 331:530-532 (SEQ ID NOs: 54-55). Examples ofspecific variants of APP include point mutation which can differ in bothposition and phenotype (for review of known variant mutation see Hardy(1992) Nature Genet. 1:233-234). All references cited here incorporatedby reference. The term “APP fragments” as used herein refers tofragments of APP other than those which consist solely of βAP or βAPfragments. That is, APP fragments will include amino acid sequences ofAPP in addition to those which form intact βAP or a fragment of βAP.

[0115] When the term “any amino acid” is used, the amino acids referredto are to be selected from the following, three letter and single letterabbreviations—which may also be used, are provided as follows:

[0116] Alanine, Ala, A; Arginine, Arg, R; Asparagine, Asn, N; Asparticacid, Asp, D; Cysteine, Cys, C; Glutamine, Gln, Q; Glutamic Acid, Glu,E; Glycine, Gly, G; Histidine, His, H; Isoleucine, Ile, I; Leucine, Leu,L; Lysine, Lys, K; Methionine, Met, M; Phenylalanine, Phe, F; Proline,Pro, P; Serine, Ser, S; Threonine, Thr, T; Tryptophan, Trp, W; Tyrosine,Tyr, Y; Valine, Val, V; Aspartic acid or Asparagine, Asx, B; Glutamicacid or Glutamine, Glx, Z; Any amino acid, Xaa, X.

[0117] The present invention describes a method to scan gene databasesfor the simple active site motif characteristic of aspartyl proteases.Eukaryotic aspartyl proteases such as pepsin and renin possess atwo-domain structure which folds to bring two aspartyl residues intoproximity within the active site. These are embedded in the shorttripeptide motif DTG, or more rarely, DSG. Most aspartyl proteases occuras proenzyme whose N-terminus must be cleaved for activation. The DTG orDSG active site motif appears at about residue 65-70 in the proenzyme(prorenin, pepsinogen), but at about residue 25-30 in the active enzymeafter cleavage of the N-terminal prodomain. The limited length of theactive site motif makes it difficult to search collections of short,expressed sequence tags (EST) for novel aspartyl proteases. ESTsequences typically average 250 nucleotides or less, and so would encode80-90 amino acid residues or less. That would be too short a sequence tospan the two active site motifs. The preferred method is to scandatabases of hypothetical or assembled protein coding sequences. Thepresent invention describes a computer method to identify candidateaspartyl proteases in protein sequence databases. The method was used toidentify seven candidate aspartyl protease sequences in theCaenorhabditis elegans genome. These sequences were then used toidentify by homology search Hu-Asp 1 and two alternative splice variantsof Hu-Asp2, designated herein as Hu-Asp2(a) and Hu-Asp2(b).

[0118] In a major aspect of the invention disclosed here we provide newinformation about APP processing. Pathogeneic processing of the amyloidprecursor protein (APP) via the Aβ pathway requires the sequentialaction of two proteases referred to as β-secretase and γ-secretase.Cleavage of APP by the β-secretase and γ-secretase generates theN-terminus and C-terninus of the Aβ peptide, respectively. Because overproduction of the Aβ peptide, particularly the Aβ₁₋₄₂, has beenimplicated in the initiation of Alzheimer's disease, inhibitors ofeither the β-secretase and/or the γ-secretase have potential in thetreatment of Alzheimer's disease. Despite the importance of theβ-secretase and γ-secretase in the pathogenic processing of APP,molecular definition of these enzymes has not been accomplished to date.That is, it was not known what enzymes were required for cleavage ateither the β-secretase or the γ-secretase cleavage site. The sitesthemselves were known because APP was known and the Aβ₁₋₄₂, peptide wasknown, see U.S. Pat. No. 5,766,846 and U.S. Pat. No. 5,837,672,(incorporated by reference, with the exception to reference to “soluble”peptides). But what enzyme was involved in producing the Aβ₁₋₄₂, peptidewas unknown.

[0119] Alignment of the amino acid sequences of Hu-Asp2 with other knownaspartyl proteases reveals a similar domain organization. All of thesequences contain a signal sequence followed by a pro-segrnent and thecatalytic domain containing 2 copies of the aspartyl protease activesite motif (DTG/DSG) separated by approximately 180 amino acid residues.Comparison of the processing site for proteolytic removal of thepro-segment in the mature forms of pepsin A, pepsin C, cathepsin D,cathepsin E and renin reveals that the mature forms of these enzymescontain between 31-35 amino acid residues upstream of the first DTGmotif. Inspection of this region in the Hu-Asp-2 amino acid sequenceindicates a preferred processing site within the sequence GRR I GS (SEQID NO: 68) as proteolytic processing of pro-protein precursors commonlyoccurs at site following dibasic amino acid pairs (eg. RR). Also,processing at this site would yield a mature enzyme with 35 amino acidresidues upstream of the first DTG, consistent with the processing sitesfor other aspartyl proteases. In the absence of self-activation ofHu-Asp2 or a knowledge of the endogenous protease that processes Hu-Asp2at this site, a recombinant form was engineered by introducing arecognition site for the PreSission protease (LEVLFQ↓GP; SEQ ID NO: 62)into the expression plasmids for bacterial, insect cell, and mammaliancell expression of pro-Hu-Asp2. In each case, the Gly residue in P1′position corresponds to the Gly residue 35 amino acids upstream of thefirst DTG motif in Hu-Asp2.

[0120] The present invention involves the molecular definition ofseveral novel human aspartyl proteases and one of these, referred to asHu-Asp-2(a) and Hu-Asp2(b), has been characterized in detail. Previousforms of asp 1 and asp 2 have been disclosed, see EP 0848062 A2 and EP0855444A2, inventors David Powel et al., assigned to Smith Kline BeechamCorp. (incorporated by reference). Herein are disclosed old and newforms of Hu-Asp 2. For the first time they are expressed in active form,their substrates are disclosed, and their specificity is disclosed.Prior to this disclosure cell or cell extracts were required to cleavethe β-secretase site, now purified protein can be used in assays, alsodescribed here. Based on the results of (1) antisense knock outexperiments, (2) transient transfection knock in experiments, and (3)biochemical experiments using purified recombinant Hu-Asp-2, wedemonstrate that Hu-Asp-2 is the β-secretase involved in the processingof APP. Although the nucleotide and predicted amino acid sequence ofHu-Asp-2(a) has been reported, see above, see EP 0848062 A2 and EP0855444A2, no functional characterization of the enzyme was disclosed.Here the authors characterize the Hu-Asp-2 enzyme and are able toexplain why it is a critical and essential enzyme required in theformation of Aβ₁₋₄₂, peptide and possible a critical step in thedevelopment of AD.

[0121] In another embodiment the present invention also describes anovel splice variant of Hu-Asp2, referred to as Hu-Asp-2(b), that hasnever before been disclosed.

[0122] In another embodiment, the invention provides isolated nucleicacid molecules comprising a polynucleotide encoding a polypeptideselected from the group consisting of human aspartyl protease 1(Hu-Asp1) and two alternative splice variants of human aspartylprotease-2 (Hu-Asp2), designated herein as Hu-Asp2(a) and Hu-Asp2(b). Asused herein, all references to “Hu-Asp2” should be understood to referto both Hu-Asp2(a) and Hu-Asp2(b). Hu-Asp1 is expressed most abundantlyin pancreas and prostate tissues, while Hu-Asp2(a) and Hu-Asp2(b) areexpressed most abundantly in pancreas and brain tissues. The inventionalso provides isolated Hu-Asp1, Hu-Asp2(a), and Hu-Asp2(b) polypeptides,as well as fragments thereof which exhibit aspartyl protease activity.

[0123] The predicted amino acid sequences of Hu-Asp1, Hu-Asp2(a) andHu-Asp2(b) share significant homology with previously identifiedmammalian aspartyl proteases such as pepsinogen A, pepsinogen B,cathepsin D, cathepsin E, and renin. P. B. Szecs, Scand. J Clin. Lab.Invest. 52: (Suppl. 2105-22 (1992)). These enzymes are characterized bythe presence of a duplicated DTG/DSG sequence motif. The Hu-Asp 1 andHuAsp2 polypeptides disclosed herein also exhibit extremely highhomology with the ProSite consensus motif for aspartyl proteasesextracted from the SwissProt database.

[0124] The nucleotide sequence given as residues 1-1554 of SEQ ID NO: 1corresponds to the nucleotide sequence encoding Hu-Asp 1, the nucleotidesequence given as residues 1-1503 of SEQ ID NO: 3 corresponds to thenucleotide sequence encoding Hu-Asp2(a), and the nucleotide sequencegiven as residues 1-1428 of SEQ ID NO: 5 corresponds to the nucleotidesequence encoding Hu-Asp2(b). The isolation and sequencing of DNAencoding Hu-Asp 1, Hu-Asp2(a), and Hu-Asp2(b) is described below inExamples 1 and 2.

[0125] As is described in Examples 1 and 2, automated sequencing methodswere used to obtain the nucleotide sequence of Hu-Asp1, Hu-Asp2(a), andHu-Asp-2(b). The Hu-Asp nucleotide sequences of the present inventionwere obtained for both DNA strands, and are believed to be 100%accurate. However, as is known in the art, nucleotide sequence obtainedby such automated methods may contain some errors. Nucleotide sequencesdetermined by automation are typically at least about 90%, moretypically at least about 95% to at least about 99.9% identical to theactual nucleotide sequence of a given nucleic acid molecule. The actualsequence may be more precisely determined using manual sequencingmethods, which are well known in the art. An error in sequence whichresults in an insertion or deletion of one or more nucleotides mayresult in a frame shift in translation such that the predicted aminoacid sequence will differ from that which would be predicted from theactual nucleotide sequence of the nucleic acid molecule, starting at thepoint of the mutation. The Hu-Asp DNA of the present invention includescDNA, chemically synthesized DNA, DNA isolated by PCR, genomic DNA, andcombinations thereof. Genomic Hu-Asp DNA may be obtained by screening agenomic library with the Hu-Asp2 cDNA described herein, using methodsthat are well known in the art, or with oligonucleotides chosen from theHu-Asp2 sequence that will prime the polymerase chain reaction (PCR).RNA transcribed from Hu-Asp DNA is also encompassed by the presentinvention.

[0126] Due to the degeneracy of the genetic code, two DNA sequences maydiffer and yet encode identical amino acid sequences. The presentinvention thus provides isolated nucleic acid molecules having apolynucleotide sequence encoding any of the Hu-Asp polypeptides of theinvention, wherein said polynucleotide sequence encodes a Hu-Asppolypeptide having the complete amino acid sequence of SEQ ID NO: 2, SEQID NO: 4, SEQ ID NO: 6, or fragments thereof.

[0127] Also provided herein are purified Hu-Asp polypeptides, bothrecombinant and non-recombinant. Most importantly, methods to produceHu-Asp2 polypeptides in active form are provided. These includeproduction of Hu-Asp2 polypeptides and variants thereof in bacterialcells, insect cells, and mammalian cells, also in forms that allowsecretion of the Hu-Asp2 polypeptide from bacterial, insect or mammaliancells into the culture medium, also methods to produce variants ofHu-Asp2 polypeptide incorporating amino acid tags that facilitatesubsequent purification. In a preferred embodiment of the invention theHu-Asp2 polypeptide is converted to a proteolytically active form eitherin transformed cells or after purification and cleavage by a secondprotease in a cell-free system, such active forms of the Hu-Asp2polypeptide beginning with the N-terminal sequence TQHGIR (SEQ ID NO:69) or ETDEEP (SEQ ID NO: 70). The sequence TQHGIR (SEQ ID NO: 69)represents the amino-terminus of Asp2(a) or Asp2(b) beginning withresidue 22 of SEQ ID NO: 4 or 6, after cleavage of a putative 21 residuesignal peptide. Recombinant Asp2(a) expressed in and purified frominsect cells was observed to have this amino terminus, presumably as aresult of cleavage by a signal peptidase. The sequence ETDEEP (SEQ IDNO: 70) represents the amino-terminus of Asp2(a) or Asp2(b) beginningwith residue 46 of SEQ ID NO: 4 or 6, as observed when Asp2(a) has beenrecombinantly produced in CHO cells (presumably after cleavage by both arodent signal peptidase and another rodent peptidase that removes apropeptide sequence). The Asp2(a) produced in the CHO cells possessesβ-secretase activity, as described in greater detail in Examples 11 and12. Variants and derivatives, including fragments, of Hu-Asp proteinshaving the native amino acid sequences given in SEQ ID Nos: 2, 4, and 6that retain any of the biological activities of Hu-Asp are also withinthe scope of the present invention. Of course, one of ordinary skill inthe art will readily be able to determine whether a variant, derivative,or fragment of a Hu-Asp protein displays Hu-Asp activity by subjectingthe variant, derivative, or fragment to a standard aspartyl proteaseassay. Fragments of Hu-Asp within the scope of this invention includethose that contain the active site domain containing the amino acidsequence DTG, fragments that contain the active site domain amino acidsequence DSG, fragments containing both the DTG and DSG active sitesequences, fragments in which the spacing of the DTG and DSG active sitesequences has been lengthened, fragments in which the spacing has beenshortened. Also within the scope of the invention are fragments ofHu-Asp in which the transmembrane domain has been removed to allowproduction of Hu-Asp2 in a soluble form. In another embodiment of theinvention, the two halves of Hu-Asp2, each containing a single activesite DTG or DSG sequence can be produced independently as recombinantpolypeptides, then combined in solution where they reconstitute anactive protease.

[0128] Thus, the invention provides a purified polypeptide comprising afragment of a mammalian Asp2 protein, wherein said fragment lacks theAsp2 transmembrane domain of said Asp2 protein, and wherein thepolypeptide and the fragment retain the β-secretase activity of saidmammalian Asp2 protein. In a preferred embodiment, the purifiedpolypeptide comprises a fragment of a human Asp2 protein that retainsthe β-secretase activity of the human Asp2 protein from which it wasderived. Examples include:

[0129] a purified polypeptide that comprises a fragment of Asp2(a)having the amino acid sequence set forth in SEQ ID NO: 4, wherein thepolypeptide lacks transmembrane domain amino acids 455 to 477 of SEQ IDNO: 4;

[0130] a purified polypeptide as described in the preceding paragraphthat further lacks cytoplasmic domain amino acids 478 to 501 of SEQ IDNO: 4;

[0131] a purified polypeptide as described in either of the precedingparagraphs that further lacks amino acids 420-454 of SEQ ID NO: 4, whichconstitute a putative alpha helical region between the catalytic domainand the transmembrane domain that is believed to be unnecessary forβ-secretase activity;

[0132] a purified polypeptide that comprises an amino acid sequence thatincludes amino acids 58 to 419 of SEQ ID NO: 4, and that lacks aminoacids 22 to 57 of SEQ ID NO: 4;

[0133] a purified polypeptide that comprises an amino acid sequence thatincludes amino acids 46 to 419 of SEQ ID NO: 4, and that lacks aminoacids 22 to 45 of SEQ ID NO: 4;

[0134] a purified polypeptide that comprises an amino acid sequence thatincludes amino acids 22 to 454 of SEQ ID NO: 4.

[0135] a purified polypeptide that comprises a fragment of Asp2(b)having the amino acid sequence set forth in SEQ ID NO: 6, and whereinsaid polypeptide lacks transmembrane domain amino acids 430 to 452 ofSEQ ID NO: 6;

[0136] a purified polypeptide as described in the preceding paragraphthat further lacks cytoplasmic domain amino acids 453 to 476 of SEQ IDNO: 6;

[0137] a purified polypeptide as described in either of the precedingtwo paragraphs that further lacks amino acids 395-429 of SEQ ID NO: 4,which constitute a putative alpha helical region between the catalyticdomain and the transmembrane domain that is believed to be unnecessaryfor β-secretase activity;

[0138] a purified polypeptide comprising an amino acid sequence thatincludes amino acids 58 to 394 of SEQ ID NO: 4, and that lacks aminoacids 22 to 57 of SEQ ID NO: 4;

[0139] a purified polypeptide comprising an amino acid sequence thatincludes amino acids 46 to 394 of SEQ ID NO: 4, and that lacks aminoacids 22 to 45 of SEQ ID NO: 4; and

[0140] a purified polypeptide comprising an amino acid sequence thatincludes amino acids 22 to 429 of SEQ ID NO: 4.

[0141] Also included as part of the invention is a purifiedpolynucleotide comprising a nucleotide sequence that encodes suchpolypeptides; a vector comprising a polynucleotide that encodes suchpolypeptides; and a host cell transformed or transfected with such apolynucleotide or vector.

[0142] Hu-Asp variants may be obtained by mutation of nativeHu-Asp-encoding nucleotide sequences, for example. A Hu-Asp variant, asreferred to herein, is a polypeptide substantially homologous to anative Hu-Asp polypeptide but which has an amino acid sequence differentfrom that of native Hu-Asp because of one or more deletions, insertions,or substitutions in the amino acid sequence. The variant amino acid ornucleotide sequence is preferably at least about 80% identical, morepreferably at least about 90% identical, and most preferably at leastabout 95% identical, to a native Hu-Asp sequence. Thus, a variantnucleotide sequence which contains, for example, 5 point mutations forevery one hundred nucleotides, as compared to a native Hu-Asp gene, willbe 95% identical to the native protein. The percentage of sequenceidentity, also termed homology, between a native and a variant Hu-Aspsequence may also be determined, for example, by comparing the twosequences using any of the computer programs commonly employed for thispurpose, such as the Gap program (Wisconsin Sequence Analysis Package,Version 8 for Unix, Genetics Computer Group, University Research Park,Madison Wisconsin), which uses the algorithm of Smith and Waterman (Adv.Appl. Math. 2: 482-489 (1981)).

[0143] Alterations of the native amino acid sequence may be accomplishedby any of a number of known techniques. For example, mutations may beintroduced at particular locations by procedures well known to theskilled artisan, such as oligonucleotide-directed mutagenesis, which isdescribed by Walder et al. (Gene 42:133 (1986)); Bauer et al. (Gene37:73 (1985)); Craik (BioTechniques, January 1985, pp. 12-19); Smith etal. (Genetic Engineering: Principles and Methods, Plenum Press (1981));and U.S. Pat. Nos. 4,518,584 and 4,737,462.

[0144] Hu-Asp variants within the scope of the invention may compriseconservatively substituted sequences, meaning that one or more aminoacid residues of a Hu-Asp polypeptide are replaced by different residuesthat do not alter the secondary and/or tertiary structure of the Hu-Asppolypeptide. Such substitutions may include the replacement of an aminoacid by a residue having similar physicochemical properties, such assubstituting one aliphatic residue (Ile, Val, Leu or Ala) for another,or substitution between basic residues Lys and Arg, acidic residues Gluand Asp, amide residues Gln and Asn, hydroxyl residues Ser and Tyr, oraromatic residues Phe and Tyr. Further information regarding makingphenotypically silent amino acid exchanges may be found in Bowie et al.,Science 247:1306-1310 (1990). Other Hu-Asp variants which might retainsubstantially the biological activities of Hu-Asp are those where aminoacid substitutions have been made in areas outside functional regions ofthe protein.

[0145] In another aspect, the invention provides an isolated nucleicacid molecule comprising a polynucleotide which hybridizes understringent conditions to a portion of the nucleic acid moleculesdescribed above, e.g., to at least about 15 nucleotides, preferably toat least about 20 nucleotides, more preferably to at least about 30nucleotides, and still more preferably to at least about from 30 to atleast about 100 nucleotides, of one of the previously described nucleicacid molecules. Such portions of nucleic acid molecules having thedescribed lengths refer to, e.g., at least about 15 contiguousnucleotides of the reference nucleic acid molecule. By stringenthybridization conditions is intended overnight incubation at about 42°C. for about 2.5 hours in 6×SSC/0.1% SDS, followed by washing of thefilters four times for 15 minutes in 1.0×SSC at 65° C., 0.1% SDS.

[0146] Fragments of the Hu-Asp encoding nucleic acid molecules describedherein, as well as polynucleotides capable of hybridizing to suchnucleic acid molecules may be used as a probe or as primers in apolymerase chain reaction (PCR). Such probes may be used, e.g., todetect the presence of Hu-Asp nucleic acids in in vitro assays, as wellas in Southern and northern blots. Cell types expressing Hu-Asp may alsobe identified by the use of such probes. Such procedures are well known,and the skilled artisan will be able to choose a probe of a lengthsuitable to the particular application. For PCR, 5′ and 3′ primerscorresponding to the termini of a desired Hu-Asp nucleic acid moleculeare employed to isolate and amplify that sequence using conventionaltechniques.

[0147] Other useful fragments of the Hu-Asp nucleic acid molecules areantisense or sense oligonucleotides comprising a single stranded nucleicacid sequence capable of binding to a target Hu-Asp mRNA (using a sensestrand), or Hu-Asp DNA (using an antisense strand) sequence. In apreferred embodiment of the invention these Hu-Asp antisenseoligonucleotides reduce Hu-Asp MRNA and consequent production of Hu-Asppolypeptides.

[0148] In another aspect, the invention includes Hu-Asp polypeptideswith or without associated native pattern glycosylation. Both Hu-Asp1and Hu-Asp2 have canonical acceptor sites for Asn-linked sugars, withHu-Asp1 having two of such sites, and Hu-Asp2 having four. Hu-Aspexpressed in yeast or mammalian expression systems (discussed below) maybe similar to or significantly different from a native Hu-Asppolypeptide in molecular weight and glycosylation pattern. Expression ofHu-Asp in bacterial expression systems will provide non-glycosylatedHu-Asp.

[0149] The polypeptides of the present invention are preferably providedin an isolated form, and preferably are substantially purified. Hu-Asppolypeptides may be recovered and purified from tissues, cultured cells,or recombinant cell cultures by well-known methods, including ammoniumsulfate or ethanol precipitation, anion or cation exchangechromatography, phosphocellulose chromatography, hydrophobic interactionchromatography, affinity chromatography, hydroxylapatite chromatography,lectin chromatography, and high performance liquid chromatography(HPLC). In a preferred embodiment, an amino acid tag is added to theHu-Asp polypeptide using genetic engineering techniques that are wellknown to practitioners of the art which include addition-of sixhistidine amino acid residues to allow purification by binding to nickelimmobilized on a suitable support, epitopes for polyclonal or monoclonalantibodies including but not limited to the T7 epitope, the myc epitope,and the V5a epitope, and fusion of Hu-Asp2 to suitable protein partnersincluding but not limited to glutathione-S-transferase or maltosebinding protein. In a preferred embodiment these additional amino acidsequences are added to the C-terminus of Hu-Asp but may be added to theN-terminus or at intervening positions within the Hu-Asp2 polypeptide.

[0150] The present invention also relates to vectors comprising thepolynucleotide molecules of the invention, as well as host celltransformed with such vectors. Any of the polynucleotide molecules ofthe invention may be joined to a vector, which generally includes aselectable marker and an origin of replication, for propagation in ahost. Because the invention also provides Hu-Asp polypeptides expressedfrom the polynucleotide molecules described above, vectors for theexpression of Hu-Asp are preferred. The vectors include DNA encoding anyof the Hu-Asp polypeptides described above or below, operably linked tosuitable transcriptional or translational regulatory sequences, such asthose derived from a mammalian, microbial, viral, or insect gene.Examples of regulatory sequences include transcriptional promoters,operators, or enhancers, mRNA ribosomal binding sites, and appropriatesequences which control transcription and translation. Nucleotidesequences are operably linked when the regulatory sequence functionallyrelates to the DNA encoding Hu-Asp. Thus, a promoter nucleotide sequenceis operably linked to a Hu-Asp DNA sequence if the promoter nucleotidesequence directs the transcription of the Hu-Asp sequence.

[0151] Selection of suitable vectors to be used for the cloning ofpolynucleotide molecules encoding Hu-Asp, or for the expression ofHu-Asp polypeptides, will of course depend upon the host cell in whichthe vector will be transformed, and, where applicable, the host cellfrom which the Hu-Asp polypeptide is to be expressed. Suitable hostcells for expression of Hu-Asp polypeptides include prokaryotes, yeast,and higher eukaryotic cells, each of which is discussed below.

[0152] The Hu-Asp polypeptides to be expressed in such host cells mayalso be fusion proteins which include regions from heterologousproteins. Such regions may be included to allow, e.g., secretion,improved stability, or facilitated purification of the polypeptide. Forexample, a sequence encoding an appropriate signal peptide can beincorporated into expression vectors. A DNA sequence for a signalpeptide (secretory leader) may be fused inframe to the Hu-Asp sequenceso that Hu-Asp is translated as a fusion protein comprising the signalpeptide. A signal peptide that is functional in the intended host cellpromotes extracellular secretion of the Hu-Asp polypeptide. Preferably,the signal sequence will be cleaved from the Hu-Asp polypeptide uponsecretion of Hu-Asp from the cell. Nonlimiting examples of signalsequences that can be used in practicing the invention include the yeastIfactor and the honeybee melatin leader in sf9 insect cells.

[0153] In a preferred embodiment, the Hu-Asp polypeptide will be afusion protein which includes a heterologous region used to facilitatepurification of the polypeptide. Many of the available peptides used forsuch a function allow selective binding of the fusion protein to abinding partner. For example, the Hu-Asp polypeptide may be modified tocomprise a peptide to form a fusion protein which specifically binds toa binding partner, or peptide tag. Nonlimiting examples of such peptidetags include the 6-His tag, thioredoxin tag, hemaglutinin tag, GST tag,and OmpA signal sequence tag. As will be understood by one of skill inthe art, the binding partner which recognizes and binds to the peptidemay be any molecule or compound including metal ions (e.g., metalaffinity columns), antibodies, or fragments thereof, and any protein orpeptide which binds the peptide, such as the FLAG tag.

[0154] Suitable host cells for expression of Hu-Asp polypeptidesincludes prokaryotes, yeast, and higher eukaryotic cells. Suitableprokaryotic hosts to be used for the expression of Hu-Asp includebacteria of the genera Escherichia, Bacillus, and Salmonella, as well asmembers of the genera Pseudomonas, Streptomyces, and Staphylococcus. Forexpression in, e.g., E. coli, a Hu-Asp polypeptide may include anN-terminal methionine residue to facilitate expression of therecombinant polypeptide in a prokaryotic host. The N-terminal Met mayoptionally then be cleaved from the expressed Hu-Asp polypeptide. OtherN-terminal amino acid residues can be added to the Hu-Asp polypeptide tofacilitate expression in Escherichia coli including but not limited tothe T7 leader sequence, the T7-caspase 8 leader sequence, as well asothers leaders including tags for purification such as the 6-His tag(Example 9). Hu-Asp polypeptides expressed in E. coli may be shortenedby removal of the cytoplasmic tail, the transmembrane domain, or themembrane proximal region. Hu-Asp polypeptides expressed in E. coli maybe obtained in either a soluble form or as an insoluble form which mayor may not be present as an inclusion body. The insoluble polypeptidemay be rendered soluble by guanidine HCl, urea or other proteindenaturants, then refolded into a soluble form before or afterpurification by dilution or dialysis into a suitable aqueous buffer. Ifthe inactive proform of the Hu-Asp was produced using recombinantmethods, it may be rendered active by cleaving off the prosegrnent witha second suitable protease such as human immunodeficiency virusprotease.

[0155] Expression vectors for use in prokaryotic hosts generallycomprises one or more phenotypic selectable marker genes. Such genesgenerally encode, e.g., a protein that confers antibiotic resistance orthat supplies an auxotrophic requirement. A wide variety of such vectorsare readily available from commercial sources. Examples include pSPORTvectors, pGEM vectors (Promega), pPROEX vectors (LTI, Bethesda, MD),Bluescript vectors (Stratagene), pET vectors (Novagen) and pQE vectors(Qiagen).

[0156] Hu-Asp may also be expressed in yeast host cells from generaincluding Saccharomyces, Pichia, and Kluveromyces. Preferred yeast hostsare S. cerevisiae and P. pastoris. Yeast vectors will often contain anorigin of replication sequence from a 2T yeast plasmid, an autonomouslyreplicating sequence (ARS), a promoter region, sequences forpolyadenylation, sequences for transcription termination, and aselectable marker gene. Vectors replicable in both yeast and E. coli(termed shuttle vectors) may also be used. In addition to theabove-mentioned features of yeast vectors, a shuttle vector will alsoinclude sequences for replication and selection in E. coli. Directsecretion of Hu-Asp polypeptides expressed in yeast hosts may beaccomplished by the inclusion of nucleotide sequence encoding the yeastI-factor leader sequence at the 5′ end of the Hu-Asp-encoding nucleotidesequence.

[0157] Insect host cell culture systems may also be used for theexpression of Hu-Asp polypeptides. In a preferred embodiment, the Hu-Asppolypeptides of the invention are expressed using an insect cellexpression system (see Example 10). Additionally, a baculovirusexpression system can be used for expression in insect cells as reviewedby Luckow and Summers, Bio/Technology 6:47 (1988).

[0158] In another preferred embodiment, the Hu-Asp polypeptide isexpressed in mammalian host cells. Nonlimiting examples of suitablemammalian cell lines include the COS7 line of monkey kidney cells(Gluzman et al, Cell 23:175 (1981)), human embyonic kidney cell line293, and Chinese hamster ovary (CHO) cells. Preferably, Chinese hamsterovary (CHO) cells are used for expression of Hu-Asp proteins (Example11).

[0159] The choice of a suitable expression vector for expression of theHu-Asp polypeptides of the invention will of course depend upon thespecific mammalian host cell to be used, and is within the skill of theordinary artisan. Examples of suitable expression vectors include pcDNA3(Invitrogen) and pSVL (Pharmacia Biotech). A preferred vector forexpression of Hu-Asp polypeptides is pcDNA3.1-Hygro (Invitrogen).Expression vectors for use in mammalian host cells may includetranscriptional and translational control sequences derived from viralgenomes. Commonly used promoter sequences and enhancer sequences whichmay be used in the present invention include, but are not limited to,those derived from human cytomegalovirus (CMV), Adenovirus 2, Polyomavirus, and Simian virus 40 (SV40). Methods for the construction ofmammalian expression vectors are disclosed, for example, in Okayama andBerg (Mol. Cell. Biol. 3:280 (1983)); Cosman et al. (Mol. Immunol.23:935 (1986)); Cosman et al. (Nature 312:768 (1984)); EP-A-0367566; andWO 91/18982.

[0160] The polypeptides of the present invention may also be used toraise polyclonal and monoclonal antibodies, which are useful indiagnostic assays for detecting Hu-Asp polypeptide expression. Suchantibodies may be prepared by conventional techniques. See, for example,Antibodies: A Laboratory Manual, Harlow and Land (eds.), Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y., (1988); MonoclonalAntibodies, Hybridomas: A New Dimension in Biological Analyses, Kennetet aL (eds.), Plenum Press, New York (1980). Synthetic peptidescomprising portions of Hu-Asp containing 5 to 20 amino acids may also beused for the production of polyclonal or monoclonal antibodies afterlinkage to a suitable carrier protein including but not limited tokeyhole limpet hemacyanin (KLH), chicken ovalbumin, or bovine serumalbumin using various cross-linking reagents including carbodimides,glutaraldehyde, or if the peptide contains a cysteine,N-methylmaleimide. A preferred peptide for immunization when conjugatedto KLH contains the C-terminus of Hu-Asp1 or Hu-Asp2 comprisingQRRPRDPEVVNDESSLVRHRWK (SEQ ID NO: 2, residues 497-518) orLRQQHDDFADDISLLK (SEQ ID NO: 4, residues 486-501), respectively. See SEQID Nos. 33-34.

[0161] The Hu-Asp nucleic acid molecules of the present invention arealso valuable for chromosome identification, as they can hybridize witha specific location on a human chromosome. Hu-Asp 1 has been localizedto chromosome 21, while Hu-Asp2 has been localized to chromosome 11q23.3-24.1. There is a current need for identifying particular sites onthe chromosome, as few chromosome marking reagents based on actualsequence data (repeat polymorphisms) are presently available for markingchromosomal location. Once a sequence has been mapped to a precisechromosomal location, the physical position of the sequence on thechromosome can be correlated with genetic map data. The relationshipbetween genes and diseases that have been mapped to the same chromosomalregion can then be identified through linkage analysis, wherein thecoinheritance of physically adjacent genes is determined.

[0162] Whether a gene appearing to be related to a particular disease isin fact the cause of the disease can then be determined by comparing thenucleic acid sequence between affected and unaffected individuals.

[0163] In another embodiment, the invention relates to a method ofassaying Hu-Asp function, specifically Hu-Asp2 function which involvesincubating in solution the Hu-Asp polypeptide with a suitable substrateincluding but not limited to a synthetic peptide containing theβ-secretase cleavage site of APP, preferably one containing the mutationfound in a Swedish kindred with inherited AD in which KM is changed toNL, such peptide comprising the sequence SEVNLDAEFR (SEQ ID NO: 63) inan acidic buffering solution, preferably an acidic buffering solution ofpH5.5 (see Example 12) using cleavage of the peptide monitored by highperformance liquid chromatography as a measure of Hu-Asp proteolyticactivity. Preferred assays for proteolytic activity utilize internallyquenched peptide assay substrates. Such suitable substrates includepeptides which have attached a paired flurophore and quencher includingbut not limited to 7-amino-4-methyl coumarin and dinitrophenol,respectively, such that cleavage of the peptide by the Hu-Asp results inincreased fluorescence due to physical separation of the flurophore andquencher. Other paired flurophores and quenchers includebodipy-tetramnethylrhodamine and QSY-5 (Molecular Probes, Inc.). In avariant of this assay, biotin or another suitable tag may be placed onone end of the peptide to anchor the peptide to a substrate assay plateand a flurophore may be placed at the other end of the peptide. Usefulflurophores include those listed above as well as Europium labels suchas W8044 (EG&g Wallac, Inc.). Cleavage of the peptide by Asp2 willrelease the flurophore or other tag from the plate, allowing compoundsto be assayed for inhibition of Asp2 proteolytic cleavage as shown by anincrease in retained fluorescence. Preferred colorimetric assays ofHu-Asp proteolytic activity utilize other suitable substrates thatinclude the P2 and P1 amino acids comprising the recognition site forcleavage linked to o-nitrophenol through an amide linkage, such thatcleavage by the Hu-Asp results in an increase in optical density afteraltering the assay buffer to alkaline pH.

[0164] In another embodiment, the invention relates to a method for theidentification of an agent that increases the activity of a Hu-Asppolypeptide selected from the group consisting of Hu-Asp1, Hu-Asp2(a),and Hu-Asp2(b), the method comprising

[0165] (a) determining the activity of said Hu-Asp polypeptide in thepresence of a test agent and in the absence of a test agent; and

[0166] (b) comparing the activity of said Hu-Asp polypeptide determinedin the presence of said test agent to the activity of said Hu-Asppolypeptide determined in the absence of said test agent; whereby ahigher level of activity in the presence of said test agent than in theabsence of said test agent indicates that said test agent has increasedthe activity of said Hu-Asp polypeptide. Such tests can be performedwith Hu-Asp polypeptide in a cell free system and with cultured cellsthat express Hu-Asp as well as variants or isoforms thereof.

[0167] In another embodiment, the invention relates to a method for theidentification of an agent that decreases the activity of a Hu-Asppolypeptide selected from the group consisting of Hu-Asp 1, Hu-Asp2(a),and Hu-Asp2(b), the method comprising

[0168] (a) determining the activity of said Hu-Asp polypeptide in thepresence of a test agent and in the absence of a test agent; and

[0169] (b) comparing the activity of said Hu-Asp polypeptide determinedin the presence of said test agent to the activity of said Hu-Asppolypeptide determined in the absence of said test agent; whereby alower level of activity in the presence of said test agent than in theabsence of said test agent indicates that said test agent has decreasedthe activity of said Hu-Asp polypeptide. Such tests can be performedwith Hu-Asp polypeptide in a cell free system and with cultured cellsthat express Hu-Asp as well as variants or isoforms thereof.

[0170] In another embodiment, the invention relates to a novel cell line(HEK125.3 cells) for measuring processing of amyloid P peptide (AP) fromthe amyloid protein precursor (APP). The cells are stable transformantsof human embryonic kidney 293 cells (HEK293) with a bicistronic vectorderived from pIRES-EGFP (Clontech) containing a modified human APP cDNA,an internal ribosome entry site and an enhanced green fluorescentprotein (EGFP) cDNA in the second cistron. The APP cDNA was modified byadding two lysine codons to the carboxyl terminus of the APP codingsequence. This increases processing of Aβ peptide from human APP by 2-4fold. This level of Aβ peptide processing is 60 fold higher than is seenin nontransformed HEK293 cells. HEK125.3 cells will be useful for assaysof compounds that inhibit Aβ peptide processing. This invention alsoincludes addition of two lysine residues to the C-terminus of other APPisoforms including the 751 and 770 amino acid isoforms, to isoforms ofAPP having mutations found in human AD including the Swedish KM→NL andV717-F mutations, to C-terminal fragments of APP, such as thosebeginning with the β-secretase cleavage site, to C-terminal fragments ofAPP containing the β-secretase cleavage site which have been operablylinked to an N-terminal signal peptide for membrane insertion andsecretion, and to C-terminal fragments of APP which have been operablylinked to an N-terminal signal peptide for membrane insertion andsecretion and a reporter sequence including but not limited to greenfluorescent protein or alkaline phosphatase, such that β-secretasecleavage releases the reporter protein from the surface of cellsexpressing the polypeptide.

[0171] Having generally described the invention, the same will be morereadily understood by reference to the following examples, which areprovided by way of illustration and are not intended as limiting.

EXAMPLE 1 Development of a Search Algorithm Useful for theIdentification of Aspartyl Proteases, and Identification of C. elegansAspartyl Protease Genes in Wormpep 12

[0172] Materials and Methods:

[0173] Classical aspartyl proteases such as pepsin and renin possess atwo-domain structure which folds to bring two aspartyl residues intoproximity within the active site. These are embedded in the shorttripeptide motif DTG, or more rarely, DSG. The DTG or DSG active sitemotif appears at about residue 25-30 in the enzyme, but at about 65-70in the proenzyme (prorenin, pepsinogen). This motif appears again about150-200 residues downstream. The proenzyme is activated by cleavage ofthe N-terminal prodomain. This pattern exemplifies the double domainstructure of the modem day aspartyl enzymes which apparently arose bygene duplication and divergence. Thus;

NH2—X—D²⁵T—Y—D^(Y+25)TG—C

[0174] where X denotes the beginning of the enzyme, following theN-terminal prodomain, and Y denotes the center of the molecule where thegene repeat begins again.

[0175] In the case of the retroviral enzymes such as the HIV protease,they represent only a half of the two-domain structures of well-knownenzymes like pepsin, cathepsin D, renin, etc. They have no prosegment,but are carved out of a polyprotein precursor containing the gag and polproteins of the virus. They can be represented by:

NH₂—D²⁵TG—C100

[0176] This “monomer” only has about 100 aa, so is extremelyparsimonious as compared to the other aspartyl protease “dimers” whichhave of the order of 330 or so aa, not counting the N-terminalprodomain.

[0177] The limited length of the eukaryotic aspartyl protease activesite motif makes it difficult to search EST collections for novelsequences. EST sequences typically average 250 nucleotides, and so inthis case would be unlikely to span both aspartyl protease active sitemotifs. Instead, we turned to the C. elegans genome. The C. elegansgenome is estimated to contain around 13,000 genes. Of these, roughly12,000 have been sequenced and the corresponding hypothetical openreading frame (ORF) has been placed in the database Wormpep12. We usedthis database as the basis for a whole genome scan of a higher eukaryotefor novel aspartyl proteases, using an algorithm that we developedspecifically for this purpose. The following AWK script for locatingproteins containing two DTG or DSG motifs was used for the search, whichwas repeated four times to recover all pairwise combinations of theaspartyl motif.

[0178] BEGIN{RS=“>”} /* defines “>” as record separator for FASTA format*/

[0179] {

[0180] pos=index($0,“DTG”) /*finds “DTG” in record*/

[0181] if (pos>0) {

[0182] rest=substr($0,pos+3) /*get rest of record after first DTG*/

[0183] pos2=index(rest,“DTG”) /*find second DTG*/

[0184] if (pos2>0) printf (“%s%s\n”,“>”,$0)} /*report hits*/

[0185] }

[0186] }

[0187] The AWK script shown above was used to search Wormpep12, whichwas downloaded from ftp.sanger.ac.uk/pub/databases/wonnpep, for sequenceentries containing at least two DTG or DSG motifs. Using AWK limitedeach record to 3000 characters or less. Thus, 35 or so larger recordswere eliminated manually from Wormpep12 as in any case these wereunlikely to encode aspartyl proteases.

[0188] Results and Discussion:

[0189] The Wormpep 12 database contains 12,178 entries, although some ofthese (<10%) represent alternatively spliced transcripts from the samegene. Estimates of the number of genes encoded in the C. elegans genomeis on the order of 13,000 genes, so Wormpep 12 may be estimated to covergreater than 90% of the C. elegans genome.

[0190] Eukaryotic aspartyl proteases contain a two-domain structure,probably arising from ancestral gene duplication. Each domain containsthe active site motif D(S/T)G located from 20-25 amino acid residuesinto each domain. The retroviral (e.g., HIV protease) or retrotransposonproteases are homodimers of subunits which are homologous to a singleeukaryotic aspartyl protease domain. An AWK script was used to searchthe Wormpep12 database for proteins in which the D(S/T)G motif occurredat least twice. This identified >60 proteins with two DTG or DSG motifs.Visual inspection was used to select proteins in which the position ofthe aspartyl domains was suggestive of a two-domain structure meetingthe criteria described above.

[0191] In addition, the PROSITE eukaryotic and viral aspartyl proteaseactive site pattern PS00141 was used to search Wormpep12 for candidateaspartyl proteases. (Bairoch A., Bucher P., Hofinann K., The PROSITEdatabase: its status in 1997, Nucleic Acids Res. 24:217-221(1997)). Thisgenerated an overlapping set of Wormpep12 sequences. Of these, sevensequences contained two DTG or DSG motifs and the PROSITE aspartylprotease active site pattern. Of these seven, three were found in thesame cosmid clone (F21F8.3, F21F8.4, and F21F8.7) suggesting that theyrepresent a family of proteins that arose by ancestral gene duplication.Two other ORFs with extensive homology to F21F8.3, F21F8.4 and F21F8.7are present in the same gene cluster (F21F8.2 and F21F8.6), however,these contain only a single DTG motif. Exhaustive BLAST searches withthese seven sequences against Wormpep 12 failed to reveal additionalcandidate aspartyl proteases in the C. elegans genome containing tworepeats of the DTG or DSG motif.

[0192] BLASTX search with each C. elegans sequence against SWISS-PROT,GenPep and TREMBL revealed that R12H7.2 was the closest worm homologueto the known mammalian aspartyl proteases, and that T18H9.2 was somewhatmore distantly related, while CEASP1, F21F8.3, F21F8.4, and F21F8.7formed a subdluster which had the least sequence homology to themammalian sequences.

[0193] Discussion:

[0194] APP, the presenilins, and p35, the activator of cdk5, all undergointracellular proteolytic processing at sites which conform to thesubstrate specificity of the HIV protease. Dysregulation of a cellularaspartyl protease with the same substrate specificity, might thereforeprovide a unifying mechanism for causation of the plaque and tanglepathologies in AD. Therefore, we sought to identify novel human aspartylproteases. A whole genome scan in C. elegans identified seven openreading frames that adhere to the aspartyl protease profile that we hadidentified. These seven aspartyl proteases probably comprise thecomplete complement of such proteases in a simple, multicellulareukaryote. These include four closely related aspartyl proteases uniqueto C. elegans which probably arose by duplication of an ancestral gene.The other three candidate aspartyl proteases (T18H9.2, R12H7.2 and C1D2.2) were found to have homology to mammalian gene sequences.

EXAMPLE 2 Identification of Novel Human Aspartyl Proteases UsingDatabase Mining by Genome Bridging

[0195] Materials and Methods:

[0196] Computer-assisted analysis of EST databases, cDNA, and predictedpolypeptide sequences:

[0197] Exhaustive homology searches of EST databases with the CEASP1,F21F8.3, F21F8.4, and F21F8.7 sequences failed to reveal any novelmammalian homologues. TBLASTN searches with RI 2H7.2 showed homology tocathepsin D, cathepsin E, pepsinogen A, pepsinogen C and renin,particularly around the DTG motif within the active site, but alsofailed to identify any additional novel mammalian aspartyl proteases.This indicates that the C. elegans genome probably contains only asingle lysosomal aspartyl protease which in mammals is represented by agene family that arose through duplication and consequent modificationof an ancestral gene.

[0198] TBLASTN searches with T18H9.2, the remaining C. elegans sequence,identified several ESTs which assembled into a contig encoding a novelhuman aspartyl protease (Hu-ASP 1). As is described above in Example 1,BLASTX search with the Hu-ASP1 contig against SWISS-PROT revealed thatthe active site motifs in the sequence aligned with the active sites ofother aspartyl proteases. Exhaustive, repetitive rounds of BLASTNsearches against LifeSeq, LifeSeqFL, and the public EST collectionsidentified 102 EST from multiple CDNA libraries that assembled into asingle contig. The 51 sequences in this contig found in public ESTcollections also have been assembled into a single contig (THC213329) byThe Institute for Genome Research (TIGR). The TIGR annotation indicatesthat they failed to find any hits in the database for the contig. Notethat the TIGR contig is the reverse complement of the LifeSeq contigthat we assembled. BLASTN search of Hu-ASP1 against the rat and mouseEST sequences in ZooSeq revealed one homologous EST in each database(Incyte clone 700311523 and IMAGE clone 313341, GenBank accession numberW10530, respectively).

[0199] TBLASTN searches with the assembled DNA sequence for Hu-ASP1against both LifeSeqFL and the public EST databases identified a second,related human sequence (Hu-Asp2) represented by a single EST (2696295).Translation of this partial cDNA sequence reveals a single DTG motifwhich has homology to the active site motif of a bovine aspartylprotease, NM1.

[0200] BLAST searches, contig assemblies and multiple sequencealignments were performed using the bioinformatics tools provided withthe LifeSeq, LifeSeqFL and LifeSeq Assembled databases from Incyte.Predicted protein motifs were identified using either the ProSitedictionary (Motifs in GCG 9) or the Pfam database.

[0201] Full-length cDNA Cloning of Hu-Asp1

[0202] The open reading frame of C. elegans gene Ti 8H9.2CE was used toquery Incyte LifeSeq and LifeSeq-FL databases and a single electronicassembly referred to as 1863920CE1 was detected. The 5′ most cDNA clonein this contig, 1863920, was obtained from Incyte and completelysequenced on both strands. Translation of the open reading framecontained within clone 1863920 revealed the presence of the duplicatedaspartyl protease active site motif (DTG/DSG) but the 5′ end wasincomplete. The remainder of the Hu-Asp 1 coding sequence was determinedby 5′ Marathon RACE analysis using a human placenta Marathon ready cDNAtemplate (Clontech). A 3′-antisense oligonucleotide primer specific forthe 5′ end of clone 1863920 was paired with the 5′-sense primer specificfor the Marathon ready cDNA synthetic adaptor in the PCR. Specific PCRproducts were directly sequenced by cycle sequencing and the resultingsequence assembled with the sequence of clone 1863920 to yield thecomplete coding sequence of Hu-Asp-1 (SEQ ID No. 1).

[0203] Several interesting features are present in the primary aminoacid sequence of Hu-Asp 1 (FIG. 1, SEQ ID No. 2). The sequence containsa signal peptide (residues 1-20 in SEQ ID No. 2), a pro-segment, and acatalytic domain containing two copies of the aspartyl protease activesite motif (DTG/DSG). The spacing between the first and second activesite motifs is about 200 residues which should correspond to theexpected size of a single, eukaryotic aspartyl protease domain. Moreinterestingly, the sequence contains a predicted transmembrane domain(residues 469-492 in SEQ ID No.2) near its C-terminus which suggeststhat the protease is anchored in the membrane. This feature is not foundin any other aspartyl protease. Cloning of a full-length Hu-Asp-2 cDNAs:

[0204] As is described above in Example 1, genome wide scan of theCaenorhabditis elegans database WormPep12 for putative aspartylproteases and subsequent mining of human EST databases revealed a humanortholog to the C. elegans gene T18H9.2 referred to as Hu-Asp 1. Theassembled contig for Hu-Asp 1 was used to query for human paralogs usingthe BLAST search tool in human EST databases and a single significantmatch (2696295CE1) with approximately 60% shared identity was found inthe LifeSeq FL database. Similar queries of either gb105PubEST or thefamily of human databases available from TIGR did not identify similarEST clones. cDNA clone 2696295, identified by single pass sequenceanalysis from a human uterus cDNA library, was obtained from Incyte andcompletely sequence on both strands. This clone contained an incomplete1266 bp open-reading frame that encoded a 422 amino acid polypeptide butlacked an initiator ATG on the 5′ end. Inspection of the predictedsequence revealed the presence of the duplicated aspartyl proteaseactive site motif DTG/DSG, separated by 194 amino acid residues.Subsequent queries of later releases of the LifeSeq EST databaseidentified an additional ESTs, sequenced from a human astrocyte cDNAlibrary (4386993), that appeared to contain additional 5′ sequencerelative to clone 2696295. Clone 4386993 was obtained from Incyte andcompletely sequenced on both strands. Comparative analysis of clone4386993 and clone 2696295 confirmed that clone 4386993 extended theopen-reading frame by 31 amino acid residues including two in-frametranslation initiation codons. Despite the presence of the two in-frameATGs, no in-frame stop codon was observed upstream of the ATG indicatingthat the 4386993 may not be full-length. Furthermore, alignment of thesequences of clones 2696295 and 4386993 revealed a 75 base pairinsertion in clone 2696295 relative to clone 4386993 that results in theinsertion of 25 additional amino acid residues in 2696295. The remainderof the Hu-Asp2 coding sequence was determined by 5′ Marathon RACEanalysis using a human hippocampus Marathon ready cDNA template(Clontech). A 3′-antisense oligonucleotide primer specific for theshared 5′-region of clones 2696295 and 4386993 was paired with the5′-sense primer specific for the Marathon ready cDNA synthetic adaptorin the PCR. Specific PCR products were directly sequenced by cyclesequencing and the resulting sequence assembled with the sequence ofclones 2696295 and 4386993 to yield the complete coding sequence ofHu-Asp2(a) (SEQ ID No. 3) and Hu-Asp2(b) (SEQ ID No. 5), respectively.

[0205] Several interesting features are present in the primary aminoacid sequence of Hu-Asp2(a) (FIG. 2 and SEQ ID No. 4) and Hu-Asp-2(b)(FIG. 3, SEQ ID No. 6). Both sequences contain a signal peptide(residues 1-21 in SEQ ID No. 4 and SEQ ID No. 6), a pro-segment, and acatalytic domain containing two copies of the aspartyl protease activesite motif (DTG/DSG). The spacing between the first and second activesite motifs is variable due to the 25 amino acid residue deletion inHu-Asp-2(b) and consists of 168-versus-194 amino acid residues, forHu-Asp2(b) and Hu-Asp-2(a), respectively. More interestingly, bothsequences contains a predicted transmembrane domain (residues 455-477 inSEQ ID No.4 and 430-452 in SEQ ID No. 6) near their C-termini whichindicates that the protease is anchored in the membrane. This feature isnot found in any other aspartyl protease except Hu-Asp1.

EXAMPLE 3 Molecular Cloning of Mouse Asp2 cDNA and Genomic DNA

[0206] Cloning and Characterization of Murine Asp2 cDNA.

[0207] The murine ortholog of Hu-Asp2 was cloned using a combination ofcDNA library screening, PCR, and genomic cloning. Approximately 500,000independent clones from a mouse brain cDNA library were screened using a³²P-labeled coding sequence probe prepared from Hu-Asp2. Replicatepositives were subjected to DNA sequence analysis and the longest cDNAcontained the entire 3′ untranslated region and 47 amino acids in thecoding region. PCR amplification of the same mouse brain cDNA librarywith an antisense oligonucleotide primer specific for the 5′-most cDNAsequence determined above and a sense primer specific for the 5′ regionof human Asp2 sequence followed by DNA sequence analysis gave anadditional 980 bp of the coding sequence. The remainder of the 5′sequence of murine Asp-2 was derived from genomic sequence (see below).

[0208] Isolation and Sequence Analysis of the Murine Asp-2 Gene.

[0209] A murine EST sequence encoding a portion of the murine Asp2 cDNAwas identified in the GenBank EST database using the BLAST search tooland the Hu-Asp2 coding sequence as the-query. Clone g3160898 displayed88% shared identity to the human sequence over 352 bp. Oligonucleotideprimer pairs specific for this region of murine Asp2 were thensynthesized and used to amplify regions of the murine gene. Murinegenomic DNA, derived from strain 129/SvJ, was amplified in the PCR (25cycles) using various primer sets specific for murine Asp2 and theproducts analyzed by agarose gel electrophoresis. The primer set Zoo-Iand Zoo-4 amplified a 750 bp fragment that contained approximately 600bp of intron sequence based on comparison to the known cDNA sequence.This primer set was then used to screen a murine BAC library by PCR, asingle genomic clone was isolated and this cloned was confirmed containthe murine Asp2 gene by DNA sequence analysis. Shotgun DNA sequencing ofthis Asp2 genomic clone and comparison to the cDNA sequences of bothHu-Asp2 and the partial murine cDNA sequences defined the full-lengthsequence of murine Asp2 (SEQ ID No. 7). The predicted amino acidsequence of murine Asp2 (SEQ ID No. 8) showed 96.4% shared identity (GCGBestFit algorithm) with 18/501 amino acid residue substitutions comparedto the human sequence (FIG. 4). The proteolytic processing of murineAsp2(a) is believed to be analogous to the processing described abovefor human Asp2(a). In addition, a variant lacking amino acid residues190-214 of SEQ ID NO: 8 is specifically contemplated as a murine Asp2(b)polypeptide. All forms of murine Asp2(b) gene and protein are intendedas aspects of the invention.

EXAMPLE 4 Tissue Distribution of Expression of Hu-Asp2 Transcripts

[0210] Materials and Methods:

[0211] The tissue distribution of expression of Hu-Asp-2 was determinedusing multiple tissue Northern blots obtained from Clontech (Palo Alto,Calif.). Incyte clone 2696295 in the vector pINCY was digested tocompletion with EcoRI/NotI and the 1.8 kb cDNA insert purified bypreparative agarose gel electrophoresis. This fragment was radiolabeledto a specific activity >1×10⁹ dpm/μg by random priming in the presenceof [α-³²P-dATP] (>3000 Ci/mmol, Amersham, Arlington Heights, Ill.) andKlenow fragment of DNA polyrnerase I. Nylon filters containingdenatured, size fractionated poly A⁺RNAs isolated from different humantissues were hybridized with 2×10⁶ dpm/ml probe in ExpressHyb buffer(Clontech, Palo Alto, Calif.) for 1 hour at 68° C. and washed asrecommended by the manufacture. Hybridization signals were visualized byautoradiography using BioMax XR film (Kodak, Rochester, N.Y.) withintensifying screens at −80° C.

[0212] Results and Discussion:

[0213] Limited information on the tissue distribution of expression ofHu-Asp-2 transcripts was obtained from database analysis due to therelatively small number of ESTs detected using the methods describedabove (<5). In an effort to gain further information on the expressionof the Hu-Asp2 gene, Northern analysis was employed to determine boththe size(s) and abundance of Hu-Asp2 transcripts. PolyA⁺RNAs isolatedfrom a series of peripheral tissues and brain regions were displayed ona solid support following separation under denaturing conditions andHu-Asp2 transcripts were visualized by high stringency hybridization toradiolabeled insert from clone 2696295. The 2696295 cDNA probevisualized a constellation of transcripts that migrated with apparentsizes of 3.0 kb, 4.4 kb and 8.0 kb with the latter two transcript beingthe most abundant.

[0214] Across the tissues surveyed, Hu-Asp2 transcripts were mostabundant in pancreas and brain with lower but detectable levels observedin all other tissues examined except thymus and PBLs. Given the relativeabundance of Hu-Asp2 transcripts in brain, the regional expression inbrain regions was also established. A similar constellation oftranscript sizes were detected in all brain regions examined[cerebellum, cerebral cortex, occipital pole, frontal lobe, temporallobe and putamen] with the highest abundance in the medulla and spinalcord.

EXAMPLE 5 Northern Blot Detection of HuAsp-1 and HuAsp-2 Transcripts inHuman Cell Lines

[0215] A variety of human cell lines were tested for their ability toproduce Hu-Asp1 and Asp2 mRNA. Human embryonic kidney (HEK-293) cells,African green monkey (Cos-7) cells, Chinese hamster ovary (CHO) cells,HELA cells, and the neuroblastoma cell line IMR-32 were all obtainedfrom the ATCC. Cells were cultured in DME containing 10% FCS except CHOcells which were maintained in α-MEM/10% FCS at 37° C. in 5% CO₂ untilthey were near confluence. Washed monolayers of cells (3×10⁷) were lysedon the dishes and poly A⁺RNA extracted using the Qiagen Oligotex DirectmRNA kit. Samples containing 2 μg of poly A⁺RNA from each cell line werefractionated under denaturing conditions (glyoxal-treated), transferredto a solid nylon membrane support by capillary action, and transcriptsvisualized by hybridization with random-primed labeled (³²P) codingsequence probes derived from either Hu-Asp1 or Hu-Asp2. Radioactivesignals were detected by exposure to X-ray film and by image analysiswith a Phosphorlmager.

[0216] The Hu-Asp1 CDNA probe visualized a similar constellation oftranscripts (2.6 kb and 3.5 kb) that were previously detected is humantissues. The relative abundance determined by quantification of theradioactive signal was Cos-7>HEK 292=HELA>IMR32.

[0217] The Hu-Asp2 cDNA probe also visualized a similar constellation oftranscripts compared to tissue (3.0 kb, 4.4 kb, and 8.0 kb) with thefollowing relative abundance; HEK 293>Cos 7>IMR32>HELA.

EXAMPLE 6 Modification of APP to Increase Aβ Processing For In VitroScreening

[0218] Human cell lines that process Aβ peptide from APP provide a meansto screen in cellular assays for inhibitors of β- and γ-secretase.Production and release of Aβ peptide into the culture supernatant ismonitored by an enzyme-linked immunosorbent assay (EIA). Althoughexpression of APP is widespread and both neural and non-neuronal celllines process and release Aβ peptide, levels of endogenous APPprocessing are low and difficult to detect by EIA. Aβ processing can beincreased by expressing in transformed cell lines mutations of APP thatenhance Aβ processing. We made the serendipitous observation thataddition of two lysine residues to the carboxyl terminus of APP695increases Aβ processing still further. This allowed us to create atransformed cell line that releases Aβ peptide into the culture mediumat the remarkable level of 20,000 pg/ml.

[0219] Materials And Methods

[0220] Materials:

[0221] Human embryonic kidney cell line 293 (HEK293 cells) were obtainedinternally. The vector pIkES-EGFP was purchased from Clontech.Oligonucleotides for mutation using the polymerase chain reaction (PCR)were purchased from Genosys. A plasmid containing human APP695 (SEQ IDNo. 9 [nucleotide] and SEQ ID No. 10 [amino acid]) was obtained fromNorthwestern University Medical School. This was subcloned into pSK(Stratagene) at the Notl site creating the plasmid pAPP695.

[0222] Mutagenesis Protocol:

[0223] The Swedish mutation (K670N, M671L) was introduced into pAPP695using the Stratagene Quick Change Mutagenesis Kit to create the plasmidpAPP695NL (SEQ ID No. 11 [nucleotide] and SEQ ID No. 12 [amino acid]).To introduce a di-lysine motif at the C-termiinus of APP695, the forwardprimer #276 5′ GACTGACCACTCGACCAGGTTC (SEQ ID No. 47) was used with the“patch” primer #274 5′CGAATTAAATTCCAGCACACTGGCTACTTCTTGTTCTGCATCTCAAAGAAC (SEQ ID No. 48) andthe flanking primer #275 CGAATTAAATTCCAGCACACTGGCTA (SEQ ID No. 49) tomodify the 3′ end of the APP695 cDNA (SEQ ID No. 15 [nucleotide] and SEQID No. 16 [amino acid]). This also added a BstX1 restriction site thatwill be compatible with the BstX1 site in the multiple cloning site ofpIRES-EGFP. PCR amplification was performed with a Clontech HF AdvantagecDNA PCR kit using the polymerase mix and buffers supplied by themanufacturer. For “patch” PCR, the patch primer was used at {fraction(1/20)}th the molar concentration of the flanking primers. PCRamplification products were purified using a QIAquick PCR purificationkit (Qiagen). After digestion with restriction enzymes, products wereseparated on 0.8% agarose gels and then excised DNA fragments werepurified using a QIAquick gel extraction kit (Qiagen).

[0224] To reassemble a modified APP695-Sw cDNA, the 5′ Not1-Bg12fragment of the APP695-Sw cDNA and the 3′ Bg12-BstX1 APP695 cDNAfragment obtained by PCR were ligated into pIRES-EGFP plasmid DNA openedat the Notl and BstX1 sites. Ligations were performed for 5 minutes atroom temperature using a Rapid DNA Ligation kit (Boehringer Mannheim)and transformed into Library Efficiency DH5a Competent Cells (GibcoBRLLife Technologies). Bacterial colonies were screened for inserts by PCRamplification using primers #276 and #275. Plasmid DNA was purified formammalian cell transfection using a QIAprep Spin Miniprep kit (Qiagen).The construct obtained was designated pMG125.3 (APPSW-KK, SEQ ID No. 17[nucleotide] and SEQ ID No. 18 [amino acid]).

[0225] Mammalian Cell Transfection:

[0226] HEK293 cells for transfection were grown to 80% confluence inDulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum.Cotransfections were performed using LipofectAmine (Gibco-BRL) with 3 μgpMG125.3 DNA and 9 μg pcDNA3.1 DNA per 10×10⁶ cells. Three daysposttransfection, cells were passaged into medium containing G418 at aconcentration of 400 μg/ml. After three days growth in selective medium,cells were sorted by their fluorescence. Clonal Selection of 125.3 cellsby FACS:

[0227] Cell samples were analyzed on an EPICS Elite ESP flow cytometer(Coulter, Hialeah, Fla.) equipped with a 488 nm excitation line suppliedby an air-cooled argon laser. EGFP emission was measured through a 525nm band-pass filter and fluorescence intensity was displayed on a4-decade log scale after gating on viable cells as determined by forwardand right angle light scatter. Single green cells were separated intoeach well of one 96 well plate containing growth medium without G418.After a four day recovery period, G418 was added to the medium to afinal concentration of 400 μg/ml. After selection, 32% of the wellscontained expanding clones. Wells with clones were expanded from the 96well plate to a 24 well plate and then a 6 well plate with the fastestgrowing colonies chosen for expansion at each passage. The final cellline selected was the fastest growing of the final six passaged. Thisclone, designated 125.3, has been maintained in G418 at 400 ug/ml withpassage every four days into fresh medium. No loss of Aβ production ofEGFP fluorescence has been seen over 23 passages.

[0228] Aβ EIA Analysis (Double Antibody Sandwich ELISA for hAβ 1-40/42):

[0229] Cell culture supernatants harvested 48 hours after transfectionwere analyzed in a standard Aβ EIA as follows. Human Aβ 1-40 or 1-42 wasmeasured using monoclonal antibody (mAb) 6E10 (Senetek, St. Louis, MO)and biotinylated rabbit antiserum 162 or 164 (New York State Institutefor Basic Research, Staten Island, N.Y.) in a double antibody sandwichELISA. The capture antibody 6E 10 is specific to an epitope present onthe N-terminal amino acid residues 1-16 of hAβ. The conjugated detectingantibodies 162 and 164 are specific for hAβ 1-40 and 1-42, respectively.Briefly, a Nunc Maxisorp 96 well immunoplate was coated with 100 μl/wellof mAb 6E10 (5μg/ml) diluted in 0.1M carbonate-bicarbonate buffer, pH9.6 and incubated at 4° C. overnight. After washing the plate 3× with0.01M DPBS (Modified Dulbecco's Phosphate Buffered Saline (0.008M sodiumphosphate, 0.002M potassium phosphate, 0.14M sodium chloride, 0.01 Mpotassium chloride, pH 7.4) from Pierce, Rockford, Ill.) containing0.05% of Tween-20 (DPBST), the plate was blocked for 60 minutes with 200μl of 10% normal sheep serum (Sigma) in 0.01M DPBS to avoid non-specificbinding. Human Aβ 1-40 or 1-42 standards 100 μl/well (Bachem, Torrance,Calif.) diluted, from a 1 mg/ml stock solution in DMSO, in culturemedium was added after washing the plate, as well as 100 μl/well ofsample, e.g., conditioned medium of transfected cells.

[0230] The plate was incubated for 2 hours at room temperature and 4° C.overnight. The next day, after washing the plate, 100 μl/wellbiotinylated rabbit antiserum 162 1:400 or 164 1:50 diluted in DPBST+0.5% BSA was added and incubated at room temperature for 1 hour, 15minutes. Following washes, 100 μl/well neutravidin-horseradishperoxidase (Pierce, Rockford, Ill.) diluted 1: 10,000 in DPBST wasapplied and incubated for 1 hour at room temperature. After the lastwashes 100 μl/well of o-phenylnediamine dihydrochloride (SigmaChemicals, St. Louis, Mo.) in 50 mM citric acid/100 mM sodium phosphatebuffer (Sigma Chemicals, St. Louis, Mo.), pH 5.0, was added as substrateand the color development was monitored at 450 nm in a kineticmicroplate reader for 20 minutes using Soft max Pro software. Allstandards and samples were run in triplicates. The samples withabsorbance values falling within the standard curve were extrapolatedfrom the standard curves using Soft max Pro software and expressed inpg/ml culture medium.

[0231] Results:

[0232] Addition of two lysine residues to the carboxyl terminus ofAPP695 greatly increases Aβ processing in HEK293 cells as shown bytransient expression (Table 1). Addition of the di-lysine motif toAPP695 increases Aβ processing to that seen with the APP695 containingthe Swedish mutation. Combining the di-lysine motif with the Swedishmutation further increases processing by an additional 2.8 fold.

[0233] Cotransformation of HEK293 cells with pMG125.3 and pcDNA3.1allowed dual selection of transformed cells for G418 resistance and highlevel expression of EGFP. After clonal selection by FACS, the cell lineobtained, produces a remarkable 20,000 pg Aβ peptide per ml of culturemedium after growth for 36 hours in 24 well plates. Production of Aβpeptide under various growth conditions is summarized in Table 2. TABLE1 Release of Aβ peptide into the culture medium 48 hours after transienttransfection of HEK293 cells with the indicated vectors containingwildtype or modified APP. Values tabulated are mean + SD and P-value forpairwise comparison using Student's t-test assuming unequal variances.Aβ 1-40 peptide APP Construct (pg/ml) Fold Increase P-value pIRES-EGFPvector 147 + 28 1.0 wt APP695 (142.3) 194 + 15 1.3 0.051 wt APP695-KK(124.1) 424 + 34 2.8 3 × 10−5 APP695-Sw (143.3) 457 + 65 3.1 2 × 10−3APP695-SwKK (125.3) 1308 + 98  8.9 3 × 10−4

[0234] TABLE 2 Release of Aβ peptide from HEK125.3 cells under variousgrowth conditions. Type of Culture Volume of Duration of Aβ 1-40 Aβ 1-42Plate Medium Culture (pg/ml) (pg/ml) 24 well plate 400 ul 36 hr 28,0361,439

EXAMPLE 7 Antisense Oligomer Inhibition of Abeta Processing in HEK125.3Cells

[0235] The sequences of Hu-Asp1 and Hu-Asp2 were provided to Sequitur,Inc (Natick, Mass.) for selection of targeted sequences and design of2nd generation chimeric antisense oligomers using prorietary technology(Sequitur Ver. D Pat pending #3002). Antisense oligomers Lot# S644,S645, S646 and S647 were targeted against Asp1. Antisense oligomers Lot#S648, S649, S650 and S651 were targeted against Asp2. Control antisenseoligomers Lot# S652, S653, S655, and S674 were targeted against anirrelevant gene and antisense oligomers Lot #S656, S657, S658, and S659were targeted against a second irrelevant gene.

[0236] For transfection with the antisense oligomers, HEK125.3 cellswere grown to about 50% confluence in 6 well plates in Minimal EssentialMedium (MEM) supplemented with 10% fetal calf serum. A stock solution ofoligofectin G (Sequitur Inc., Natick, Mass.) at 2 mg/ml was diluted to50 μg/ml in serum free MEM. Separately, the antisense oligomer stocksolution at 100 μM was diluted to 800 nM in Opti-MEM (GIBCO-BRL, GrandIsland, N.Y.). The diluted stocks of oligofectin G and antisenseoligomer were then mixed at a ratio of 1:1 and incubated at roomtemperature. After 15 minutes incubation, the reagent was diluted 10fold into MEM containing 10% fetal calf serum and 2 ml was added to eachwell of the 6 well plate after first removing the old medium. Aftertransfection, cells were grown in the continual presence of theoligofectin G/antisense oligomer. To monitor Aβ peptide release, 400 μlof conditioned medium was removed periodically from the culture well andreplaced with fresh medium beginning 24 hours after transfection. APpeptides in the conditioned medium were assayed via immunoprecipitationand Western blotting. Data reported are from culture supernatantsharvested 48 hours after transfection.

[0237] The 16 different antisense oligomers obtained from Sequitur Inc.were transfected separately into HEK125.3 cells to determine theiraffect on Aβ peptide processing. Only antisense oligomers targetedagainst Asp2 significantly reduced Abeta processing by HEK125.3 cells.Both Aβ (1-40) and Aβ (1-42) were inhibited by the same degree. In Table3, percent inhibition is calculated with respect to untransfected cells.Antisense oligomer reagents giving greater than 50% inhibition aremarked with an asterisk. For ASP2, 4 of 4 antisense oligomers gavegreater than 50% inhibition with an average inhibition of 62% for Aβ1-40 processing and 60% for Aβ 1-42 processing. TABLE 3 Inhibition of Aβpeptide release from HEK125.3 cells treated with antisense oligomers.Gene Targeted Antisense Oligomer Abeta (1-40) Abeta (1-42) Asp2-1 S64871%* 67%* Asp2-2 S649 83%* 76%* Asp2-3 S650 46%* 50%* Asp2-4 S651 47%*46%* Con1-1 S652 13% 18% Con1-2 S653 35% 30% Con1-3 S655 9% 18% Con1-4S674 29% 18% Con2-1 S656 12% 18% Con2-2 S657 16% 19% Con2-3 S658 8% 35%Con2-4 S659 3% 18%

[0238] Since HEK293 cells derive from kidney, the experiment wasextended to human IMR-32 neuroblastoma cells which express all three APPisoforms and which release Aβ peptides into conditioned medium atmeasurable levels. [See Neill et al., J. NeuroSci. Res., (1994) 39:482-93; and Asami-Odaka et al., Biochem., (1995) 34:10272-8.]Essentially identical results were obtained in the neuroblastoma cellsas the HEK293 cells. As shown in Table 3B, the pair of Asp2 antisenseoligomers reduced Asp2 MRNA by roughly one-half, while the pair ofreverse control oligomers lacked this effect (Table 3B). TABLE 3BReduction of Aβ40 and Aβ42 in human neuroblastoma IMR-32 cells and mouseneuroblastoma Neuro-2A cells treated with Asp2 antisense and controloligomers as indicated. Oligomers were transfected in quadruplicatecultures. Values tabulated are normalized against cultures treated witholigofectin-G ™ only (mean + SD, ** p < 0.001 compared to reversecontrol oligomer). Asp2 IMR-32 cells Neuro-2A cells mRNA Aβ40 Aβ42 Aβ40Aβ42 Asp2-1A −75% −49 + 2%** −42 + 14%** −70 + −67 + 2%** 7%** Asp2-1R0.16 −0 + 3% 21.26 −9 + 15% 1.05 Asp2-2A −39% −43 + 3%** −44 + 18%** −61−61 + 12%** + 12%** Asp2-2R 0.47 12.2 19.22 6.15 −8 + 10%

[0239] Together with the reduction in Asp2 mRNA there was a concomitantreduction in the release of Aβ40 and Aβ42 peptides into the conditionedmedium. Thus, Asp2 functions directly or indirectly in a human kidneyand a human neuroblastoma cell line to facilitate the processing of APPinto Aβ peptides. Molecular cloning of the mouse Asp2 cDNA revealed ahigh degree of homology to human (>96% amino acid identity, see Example3), and indeed, complete nucleotide identity at the sites targeted bythe Asp2-1A and Asp2-2A antisense oligomers. Similar results wereobtained in mouse Neuro-2a cells engineered to express APP-Sw-KK. TheAsp2 antisense oligomers reduced release of Aβ peptides into the mediumwhile the reverse control oligomers did not (Table 3B). Thus, the threeantisense experiments with HEK293, IMR-32 and Neuro-2a cells indicatethat Asp2 acts directly or indirectly to facilitate Aβ processing inboth somatic and neural cell lines.

EXAMPLE 8 Demonstration of Hu-Asp2 β-Secretase Activity in CulturedCells

[0240] Several mutations in APP associated with early onset Alzheimer'sdisease have been shown to alter Aβ peptide processing. These flankthe—and C-terminal cleavage sites that release Aβ from APP. Thesecleavage sites are referred to as the β-secretase and γ-secretasecleavage sites, respectively. Cleavage of APP at the β-secretase sitecreates a C-terminal fragment of APP containing 99 amino acids of 11,145daltons molecular weight. The Swedish KM→NL mutation immediatelyupstream of the β-secretase cleavage site causes a general increase inproduction of both the 1-40 and 1-42 amino acid forms of Aβ peptide. TheLondon VF mutation (V717-F in the APP770 isoform) has little effect ontotal Aβ peptide production, but appears to preferentially increase thepercentage of the longer 1-42 amino acid form of Aβ peptide by affectingthe choice of β-secretase cleavage site used during APP processing.Thus, we sought to determine if these mutations altered the amount andtype of Aβ peptide produced by cultured cells cotransfected with aconstruct directing expression of Hu-Asp2.

[0241] Two experiments were performed which demonstrate Hu-Asp2β-secretase activity in cultured cells. In the first experiment,treatment of HEK125.3 cells with antisense oligomers directed againstHu-Asp2 transcripts as described in Example 7 was found to decrease theamount of the C-terminal fragment of APP created by β-secretase cleavage(CTF99) (FIG. 9). This shows that Hu-Asp2 acts directly or indirectly tofacilitate β-secretase cleavage. In the second experiment, increasedexpression of Hu-Asp2 in transfected mouse Neuro2A cells is shown toincrease accumulation of the CTF99 β-secretase cleavage fragment (FIG.10). This increase is seen most easily when a mutant APP-KK clonecontaining a C-terminal di-lysine motif is used for transfection. Afurther increase is seen when Hu-Asp2 is cotransfected with APP-Sw-KKcontaining the Swedish mutation KM→NL. The Swedish mutation is known toincrease cleavage of APP by the β-secretase.

[0242] A second set of experiments demonstrate Hu-Asp2 facilitatesγ-secretase activity in cotransfection experiments with human embryonickidney HEK293 cells. Cotransfection of Hu-Asp2 with an APP-KK clonegreatly increases production and release of soluble Aβ1-40 and Aβ1-42peptides from HEK293 cells. There is a proportionately greater increasein the release of Aβ 1-42. A further increase in production of Aβ1-42 isseen when Hu-Asp2 is cotransfected with APP-VF (SEQ ID No. 13[nucleotide] and SEQ ID No. 14 [amino acid]) or APP-VF-KK SEQ ID No. 19[nucleotide] and SEQ ID No. 20 [amino acid]) clones containing theLondon mutation V717-F. The V717-F mutation is known to alter cleavagespecificity of the APP γ-secretase such that the preference for cleavageat the Aβ42 site is increased. Thus, Asp2 acts directly or indirectly tofacilitate γ-secretase processing of APP at the P42 cleavage site.

[0243] Materials

[0244] Antibodies 6E10 and 4G8 were purchased from Senetek (St. Louis,Mo.). Antibody 369 was obtained from the laboratory of Paul Greengard atthe Rockefeller University. Antibody C8 was obtained from the laboratoryof Dennis Selkoe at the Harvard Medical School and Brigham and Women'sHospital.

[0245] APP Constructs Used

[0246] The APP constructs used for transfection experiments comprisedthe following

[0247] APP: wild-type APP695 (SEQ ID No. 9 and No. 10)

[0248] APP-Sw: APP695 containing the Swedish KM→NL mutation (SEQ ID No.11 and No. 12 , wherein the lysine (K) at residue 595 of APP695 ischanged to asparagine (N) and the methionine (M) at residue 596 ofAPP695 is changed to leucine (L).),

[0249] APP-VF: APP695 containing the London V→F mutation (SEQ ID Nos. 13& 14) (Affected residue 717 of the -APP770 isoform corresponds withresidue 642 of the APP695 isoform. Thus, APP-VF as set in SEQ ID NO: 14comprises the APP695 sequence, wherein the valine (V) at residue 642 ischanged to phenylalanine (F).)

[0250] APP-KK: APP695 containing a C-terminal KK motif (SEQ ID Nos. 15 &16),

[0251] APP-Sw-KK: APP695-Sw containing a C-terminal KK motif (SEQ ID No.17 & 18),

[0252] APP-VF-KK: APP695-VF containing a C-terminal KK motif (SEQ IDNos. 19&20).

[0253] These were inserted into the vector pIRES-EGFP (Clontech, PaloAlto Calif.) between the Not1 and BstX1 sites using appropriate linkersequences introduced by PCR.

[0254] Transfection of Antisense Oligomers or Plasmid DNA Constructs inHEK293 Cells, HEK125.3 Cells and Neuro-2A Cells,

[0255] Human embryonic kidney HEK293 cells and mouse Neuro-2a cells weretransfected with expression constructs using the Lipofectamine Plusreagent from Gibco/BRL. Cells were seeded in 24 well tissue cultureplates to a density of 70-80% confluence. Four wells per plate weretransfected with 2 μg DNA (3: 1, APP:cotransfectant), 8 μl Plus reagent,and 4 μl Lipofectamine in OptiMEM. OptiMEM was added to a total volumeof 1 ml, distributed 200 μl per well and incubated 3 hours. Care wastaken to hold constant the ratios of the two plasmids used forcotransfection as well as the total amount of DNA used in thetransfection. The transfection media was replaced with DMEM, 10%FBS,NaPyruvate, with antibiotic/antimycotic and the cells were incubatedunder normal conditions (37° C., 5% CO₂) for 48 hours. The conditionedmedia were removed to polypropylene tubes and stored at −80° C. untilassayed for the content of Aβ1-40 and Aβ1-42 by EIA as described in thepreceding examples. Transfection of antisense oligomers into HEK125.3cells was as described in Example 7.

[0256] Preparation of Cell Extracts, Western Blot Protocol

[0257] Cells were harvested after being transfected with plasmid DNA forabout 60 hours. First, cells were transferred to 15-ml conical tube fromthe plate and centrifuged at 1,500 rpm for 5 minutes to remove themedium. The cell pellets were washed once with PBS. We then lysed thecells with lysis buffer (10 mM HEPES, pH 7.9, 150 mM NaCl, 10% glycerol,1 mM EGTA, 1 mM EDTA, 0.1 mM sodium vanadate and 1% NP-40). The lysedcell mixtures were centrifuged at 5000 rpm and the supernatant wasstored at −20° C. as the cell extracts. Equal amounts of extracts fromHEK125.3 cells transfected with the Asp2 antisense oligomers andcontrols were precipitated with antibody 369 that recognizes theC-terminus of APP and then CTF99 was detected in the immunoprecipitatewith antibody 6E10. The experiment was repeated using C8, a secondprecipitating antibody that also recognizes the C-terminus of APP. ForWestern blot of extracts from mouse Neuro-2a cells cotransfected withHu-Asp2 and APP-KK, APP-Sw-KK, APP-VF-KK or APP-VF, equal amounts ofcell extracts were electrophoresed through 4-10% or 10-20% Tricinegradient gels (NOVEX, San Diego, Calif.). Full length APP and the CTF99β-secretase product were detected with antibody 6E 10.

[0258] Results

[0259] Transfection of HEK125.3 cells with Asp2-1 or Asp2-2 antisenseoligomers reduces production of the CTF β-secretase product incomparison to cells similarly transfected with control oligomers havingthe reverse sequence (Asp2-1 reverse & Asp2-2 reverse), see FIG. 9.Correspondingly, cotransfection of Hu-Asp2 into mouse Neuro-2a cellswith the APP-KK construct increased the formation of CTF99. (See FIG.10.) This was further increased if Hu-Asp2 was coexpressed withAPP-Sw-KK, a mutant form of APP containing the Swedish KM→NL mutationthat increases β-secretase processing.

[0260] Effects of Asp2 on the production of Ab peptides fromendogenously expressed APP isoforms were assessed in HEK293 cellstransfected with a construct expressing Asp2 or with the empty vectorafter selection of transformants with the antibiotic G418. Aβ40production was increased in cells transformed with the Asp2 construct incomparison to those transformed with the empty vector DNA. Aβ40 levelsin conditioned medium collected from the Asp2 transformed and controlcultures was 424+45 pg /ml and 113+58 pg/ml, respectively (p<0.001).Aβ42 release was below the limit of detection by the EIA, while therelease of sAPPa was unaffected, 112±8 ng/ml versus 111±40 ng/ml. Thisfurther indicates that Asp2 acts directly or indirectly to facilitatethe processing and release of Aβ from endogenously expressed APP.

[0261] Co-transfection of Hu-Asp2 with APP has little effect on Aβ40production but increases Aβ42 production above background (Table 4).Addition of the di-lysine motif to the C-terminus of APP increases Aβpeptide processing about two fold, although Aβ40 and Aβ42 productionremain quite low (352 pg/ml and 21 pg/ml, respectively). Cotransfectionof Asp2 with APP-KK further increases both Aβ40 and Aβ42 production.

[0262] The APP V717-F mutation has been shown to increase γ-secretaseprocessing at the Aβ42 cleavage site. Cotransfection of Hu-Asp2 with theAPP-VF or APP-VF-KK constructs increased Aβ42 production (a two foldincrease with APP-VF and a four-fold increase with APP-VF-KK, Table 4),but had mixed effects on Aβ40 production (a slight decrease with APP-VF,and a two fold increase with APP-VF-KK in comparison to the pcDNAcotransfection control. Thus, the effect of Asp2 on Aβ42 production wasproportionately greater leading to an increase in the ratio ofAβ42/total Ab. Indeed, the ratio of Aβ42/total AP reaches a very highvalue of 42% in HEK293 cells cotransfected with Hu-Asp2 and APP-VF-KK.TABLE 4 Results of cotransfecting Hu-Asp2 or pcDNA plasmid DNA withvarious APP constructs containing the V717-F mutation that modifiesγ-secretase processing. Cotransfection with Asp2 consistently increasesthe ratio of Aβ42/total Aβ. Values tabulated are Aβ peptide pg/ml. pcDNAAsp2 Cotransfection Cotransfection Aβ40 Aβ42 Aβ42/Total Aβ40 Aβ42Aβ42/Total APP 192 ± 18 <4 <2% 188 ± 40  8 ± 10 3.9% APP-VF 118 ± 15 15± 19 11.5% 85 ± 7  24 ± 12 22.4% APP-KK 352 ± 24 21 ± 6  5.5% 1062 ± 101226 ± 49 17.5% APP-VF-KK 230 ± 31 88 ± 24 27.7% 491 ± 35 355 ± 36 42%

EXAMPLE 9 Bacterial Expression of Human Asp2(a)

[0263] Expression of Recombinant Hu-Asp2(a) in E. coli.

[0264] Hu-Asp2(a) can be expressed in E. coli after addition ofN-terminal sequences such as a T7 tag (SEQ ID No. 21 and No. 22) or a T7tag followed by a caspase 8 leader sequence (SEQ ID No. 23 and No. 24).Alternatively, reduction of the GC content of the 5′ sequence by sitedirected mutagenesis can be used to increase the yield of Hu-Asp2 (SEQID No. 25 and No. 26). In addition, Asp2(a) can be engineered with aproteolytic cleavage site (SEQ ID No. 27 and No. 28). To produce asoluble protein after expression and refolding, deletion of thetransmembrane domain and cytoplasmic tail, or deletion of the membraneproximal region, transmembrane domain, and cytoplasmic tail ispreferred. Any materials (vectors, host cells, etc.) and methodsdescribed herein to express Hu-Asp2(a) should in principle be equallyeffective for expression of Hu-Asp2(b).

[0265] Methods

[0266] PCR with primers containing appropriate linker sequences was usedto assemble fusions of Asp2(a) coding sequence with N-terminal sequencemodifications including a T7 tag (SEQ ID Nos. 21 and 22) or a T7-caspase8 leader (SEQ ID Nos. 23 and 24). These constructs were cloned into theexpression vector pet23a(+) [Novagen] in which a T7 promoter directsexpression of a T7 tag preceding a sequence of multiple cloning sites.To clone Hu-Asp2 sequences behind the T7 leader of pet23a+, thefollowing oligonucleotides were used for amplification of the selectedHu-Asp2(a) sequence: #553=GTGGATCCACCCAGCACGGCATCCGGCTG (SEQ ID No. 35),#554=GAAAGCTTTCATGACTCATCTGTCTGTGGAATGTTG (SEQ ID No. 36) which placedBamHI and HindIII sites flanking the 5′ and 3′ ends of the insert,respectively. The Asp2(a) sequence was amplified from the full lengthAsp2(a) cDNA cloned into pcDNA3.1 using the Advantage-GC cDNA PCR[Clontech] following the manufacturer's supplied protocol usingannealing & extension at 68° C. in a two-step PCR cycle for 25 cycles.The insert and vector were cut with BamHI and HindlIl, purified byelectrophoresis through an agarose gel, then ligated using the Rapid DNALigation kit [Boerhinger Mannheim]. The ligation reaction was used totransform the E. coli strain JM109 (Promega) and colonies were pickedfor the purification of plasmid (Qiagen,Qiaprep minispin) and DNAsequence analysis. For inducible expression using induction withisopropyl b-D-thiogalactopyranoside (JPTG), the expression vector wastransferred into E. coli strain BL21 (Statagene). Bacterial cultureswere grown in LB broth in the presence of ampicillin at 100 ug/ml, andinduced in log phase growth at an OD600 of 0.6-1.0 with 1 mM IPTG for 4hour at 37° C. The cell pellet was harvested by centriftigation.

[0267] To clone Hu-Asp2 sequences behind the T7 tag and caspase leader(SEQ ID Nos. 23 and 24), the construct created above containing theT7-Hu-Asp2 sequence (SEQ ID Nos. 21 and 22) was opened at the BamHIsite, and then the phosphorylated caspase 8 leader oligonucleotides#559=GATCGATGACTATCTCTGACTCTCCGCGTGAACAGGACG (SEQ ID No. 37),#560=GATCCGTCCTGTTCACGCGGAGAGTCAGAGATAGTCATC (SEQ ID No.38) wereannealed and ligated to the vector DNA. The 5′ overhang for each set ofoligonucleotides was designed such that it allowed ligation into theBamHI site but not subsequent digestion with BamHI. The ligationreaction was transformed into JM109 as above for analysis of proteinexpression after transfer to E. coli strain BL21.

[0268] In order to reduce the GC content of the 5′ terminus of asp2(a),a pair of antiparallel oligos were designed to change degenerate codonbases in 15 amino acid positions from G/C to A/T (SEQ ID Nos. 25 and26). The new nucleotide sequence at the 5′ end of asp2 did not changethe encoded amino acid and was chosen to optimize E. Coli expression.The sequence of the sense linker is 5′CGGCATCCGGCTGCCCCTGCGTAGCGGTCTGGGTGGTGCTCCACTGGGTCTGCGTCTGCCCCGGGAGACCGACGAA G 3′ (SEQ ID No.39). The sequence of theantisense linker is : 5′CTTCGTCGGTCTCCCGGGGCAGACGCAGACCCAGTGGAGCACCACCCAGACCGCTACGCAGGGGCAGCCGGATGCCG 3′ (SEQ ID No.40). After annealing thephosphorylated linkers together in 0.1 M NaCl-10 mM Tris, pH 7.4 theywere ligated into unique Cla I and Sma I sites in Hu-Asp2 in the vectorpTAC. For inducible expression using induction with isopropylb-D-thiogalactopyranoside (IPTG), bacterial cultures were grown in LBbroth in the presence of ampicillin at 100 ug/ml, and induced in logphase growth at an OD600 of 0.6-1.0 with 1 mM IPTG for 4 hour at 37° C.The cell pellet was harvested by centrifugation.

[0269] To create a vector in which the leader sequences can be removedby limited proteolysis with caspase 8 such that this liberates a Hu-Asp2polypeptide beginning with the N-terminal sequence GSFV (SEQ ID Nos. 27and 28), the following procedure was followed. Two phosphorylatedoligonucleotides containing the caspase 8 cleavage site EETD, #571=5′GATCGATGACTATCTCTGACTCTCCGCTGGACTCTGGTATCGAAACCGACG (SEQ ID No. 41) and#572=GATCCGTCGGTTTCGATACCAGAGTCCAGCGGAGAGTCAGAGATAGTCAT C (SEQ ID No.42) were annealed and ligated into pET23a+that had been opened withBamHI. After transformation into JM109, the purified vector DNA wasrecovered and orientation of the insert was confirmed by DNA sequenceanalysis.

[0270] The following oligonucleotides were used for amplification of theselected Hu-Asp2(a) sequence: #573=5′AAGGATCCTTTGTGGAGATGGTGGACAACCTG,(SEQ ID No. 43) #554=GAAAGCTTTCATGACTCATCTGTCTGTGGAATGTTG (SEQ ID No.44) which placed BamHI and HindHi sites flanking the 5′ and 3′ ends ofthe insert, respectively. The Hu-Asp2(a) sequence was amplified from thefull length Hu-Asp2(a) cDNA cloned into pcDNA3.1 using the Advantage-GCcDNA PCR [Clontech] following the manufacturer's supplied protocol usingannealing & extension at 68° C. in a two-step PCR cycle for 25 cycles.The insert and vector were cut with BamHI and HindIII, purified byelectrophoresis through an agarose gel, then ligated using the Rapid DNALigation kit [Boerhinger Mannheim]. The ligation reaction was used totransform the E. coli strain JM109 [Promega] and colonies were pickedfor the purification of plasmid (Qiagen,Qiaprep minispin) and DNAsequence analysis. For inducible expression using induction withisopropyl b-D-thiogalactopyranoside (IPTG), the expression vector wastransferred into E. Coli strain BL21 (Statagene). Bacterial cultureswere grown in LB broth in the presence of ampicillin at 100 ug/ml, andinduced in log phase growth at an OD600 of 0.6-1.0 with 1 mM IPTG for 4hour at 37° C. The cell pellet was harvested by centrifugation.

[0271] To assist purification, a 6-His tag can be introduced into any ofthe above constructs following the T7 leader by opening the construct atthe BamHI site and then ligating in the annealed, phosphorylatedoligonucleotides containing the six histidine sequence#565=GATCGCATCATCACCATCACCATG (SEQ ID No. 45),#566=GATCCATGGTGATGGTGATGATGC (SEQ ID No. 46). The 5′ overhang for eachset of oligonucleotides was designed such that it allowed ligation intothe BaniHI site but not subsequent digestion with BamHI.

[0272] Preparation ofBacterial Pellet:

[0273] 36.34g of bacterial pellet representing 10.8L of growth wasdispersed into a total volume of 200 ml using a 20 mm tissue homogenizerprobe at 3000 to 5000 rpm in 2M KCl, 0.1M Tris, 0.05M EDTA, ImM DTT. Theconductivity adjusted to about 193 mMhos with water. After the pelletwas dispersed, an additional amount of the KCl solution was added,bringing the total volume to 500 ml. This suspension was homogenizedfurther for about 3 minutes at 5000 rpm using the same probe. Themixture was then passed through a Rannie high-pressure homogenizer at10,000 psi.

[0274] In all cases, the pellet material was carried forward, while thesoluble fraction was discarded. The resultant solution was centrifugedin a GSA rotor for 1 hour at 12,500 rpm. The pellet was resuspended inthe same solution (without the DTT) using the same tissue homogenizerprobe at 2,000 rpm. After homogenizing for 5 minutes at 3000 rpm, thevolume was adjusted to 500 ml with the same solution, and spun for 1hour at 12,500 rpm. The pellet was then resuspended as before, but thistime the final volume was adjusted to 1.5L with the same solution priorto homogenizing for 5 minutes. After centrifuging at the same speed for30 minutes, this procedure was repeated. The pellet was then resuspendedinto about 150 ml of cold water, pooling the pellets from the sixcentrifuge tubes used in the GSA rotor. The pellet has homogenized for 5minutes at 3,000 rpm, volume adjusted to 250 ml with cold water, thenspun for 30 minutes. Weight of the resultant pellet was 17.75 g.

[0275] Summary: Lysis of bacterial pellet in KCl solution, followed bycentrifugation in a GSA rotor was used to initially prepare the pellet.The same solution was then used an additional three times forresuspension/homogenization. A final water wash/homogenization was thenperformed to remove excess KCl and EDTA.

[0276] Solublization ofRecombinant Hu-Asp2(a):

[0277] A ratio of 9-10ml/gram of pellet was utilized for solubilizingthe rHuAsp2L from the pellet previously described. 17.75g of pellet wasthawed, and 150 ml of 8M guanidine HCl, 5 mM PME, 0.1% DEA, was added.3M Tris was used to titrate the pH to 8.6. The pellet was initiallyresuspended into the guanidine solution using a 20 mm tissue homogenizerprobe at 1000 rpm. The mixture was then stirred at 4° C. for 1 hourprior to centrifugation at 12,500 rpm for 1 hour in GSA rotor. Theresultant supernatant was then centrifuged for 30 minutes at 40,000×g inan SS-34 rotor. The final supemnatant was then stored at −20° C., exceptfor 50 ml.

[0278] Immobilized Nickel Affinity Chromatography of SolubilizedRecombinant Hu-Asp2(a):

[0279] The following solutions were utilized:

[0280] A) 6M Guanidine HCl, O.1M NaP, pH 8.0, 0.01M Tris, 5 mM PME, 0.5mM Imidazole

[0281] A′) 6M Urea, 20 mM NaP, pH 6.80, 50 mM NaCl

[0282] B′) 6M Urea, 20 mM NaP, pH 6.20,50 mM NaCl, 2 mM Imidazole

[0283] C′) 6M Urea, 20 mM NaP, pH 6.80, 50 mM NaCl, 300 mM Imidazole

[0284] Note: Buffers A′ and C′ were mixed at the appropriate ratios togive intermediate concentrations of Imidazole.

[0285] The 50 ml of solubilized material was combined with 50 ml ofbuffer A prior to adding to 100-125 ml Qiagen Ni-NTA SuperFlow(pre-equilibrated with buffer A) in a 5×10 cm Bio-Rad econo column. Thiswas shaken gently overnight at 4° C. in the cold room.

[0286] Chromatography Steps:

[0287] Drained the resultant flow through.

[0288] Washed with 50 ml buffer A (collecting into flow throughfraction)

[0289] Washed with 250 ml buffer A (wash 1)

[0290] Washed with 250 ml buffer A (wash 2)

[0291] Washed with 250 ml buffer A′

[0292] Washed with 250 ml buffer B′

[0293] Washed with 250 ml buffer A′

[0294] Eluted with 250 ml 75 mM Imidazole

[0295] Eluted with 250 ml l50 mM Imidazole (150-1)

[0296] Eluted with 250 ml l50 mM Imidazole (150-2)

[0297] Eluted with 250 ml 300 mM Imidazole (300-1)

[0298] Eluted with 250 ml 300 mM liidazole (300-2)

[0299] Eluted with 250 ml 300 mM Imidazole (300-3)

[0300] Chromatography Results:

[0301] The Hu-Asp(a) eluted at 75 mM Imidazole through 300 mM Imidazole.The 75 mM fraction, as well as the first l50 mM Imidazole (150-1)fraction contained contaminating proteins as visualized on CoomassieBlue stained gels. Therefore, fractions 150-2 and 300-1 will be utilizedfor refolding experiments since they contained the greatest amount ofprotein as visualized on a Coomassie Blue stained gel.

[0302] Refolding Experiments of Recombinant Hu-Asp2(a):

[0303] Experiment 1:

[0304] Forty ml of 150-2 was spiked with 1M DTT, 3M Tris, pH 7.4 and DEAto a final concentration of 6 mM, 50 mM, and 0.1% respectively. This wasdiluted suddenly (while stirring) with 200 ml of (4° C.) cold 2OmM NaP,pH 6.8, 150 mM NaCl. This dilution gave a final Urea concentration of lM. This solution remained clear, even if allowed to set open to the airat room temperature (RT) or at 4° C.

[0305] After setting open to the air for 4-5 hours at 4° C., thissolution was then dialyzed overnight against 20 mM NaP, pH 7.4, 15OmMNaCl, 20% glycerol. This method effectively removes the urea in thesolution without precipitation of the protein.

[0306] Experiment 2:

[0307] Some of the 150-2 eluate was concentrated 2× on an AmiconCentriprep, 10,000 MWCO, then treated as in Experiment 1. This materialalso stayed in solution, with no visible precipitation.

[0308] Experiment 3:

[0309] 89 ml of the 150-2 eluate was spiked with IM DTT, 3M Tris, pH 7.4and DEA to a final concentration of 6 mM, 50 mM, and 0.1% respectively.This was diluted suddenly (while stirring) with 445 ml of (4° C.) cold20 mM NaP, pH 6.8, 150 mM NaCl. This solution appeared clear, with noapparent precipitation. The solution was removed to RT and stirred for10 minutes prior to adding MEA to a final concentration of 0.1 mM. Thiswas stirred slowly at RT for 1 hour. Cystamine and CuSO₄ were then addedto final concentrations of 1 mM and 10 μM respectively. The solution wasstirred slowly at RT for 10 minutes prior to being moved to the 4° C.cold room and shaken slowly overnight, open to the air.

[0310] The following day, the solution (still clear, with no apparentprecipitation) was centrifuged at 100,000× g for 1 hour. Supernatantsfrom multiple runs were pooled, and the bulk of the stabilized proteinwas dialyzed against 20 mM NaP, pH 7.4, 150 nmM NaCl, 20% glycerol.After dialysis, the material was stored at −20° C.

[0311] Some (about 10 ml) of the protein solution (still in 1 M Urea)was saved back for biochemical analyses, and frozen at −20° C. forstorage.

EXAMPLE 10 Expression of Hu-Asp2 and Derivatives in Insect Cells

[0312] Any materials (vectors, host cells, etc.) and methods that areuseful to express Hu-Asp2(a) should in principle be equally effectivefor expression of Hu-Asp2(b).

[0313] Expression by Baculovirus Infection.

[0314] The coding sequence of Hu-Asp2(a) and Hu-ASp2(b) and severalderivatives were engineered for expression in insect cells using thePCR. For the full-length sequence, a 5′-sense oligonucleotide primerthat modified the translation initiation site to fit the Kozak consensussequence was paired with a 3′-antisense primer that contains the naturaltranslation termination codon in the Hu-Asp2 sequence. PCR amplificationof the pcDNA3. 1(hygro)/Hu-Asp2(a) template was used to prepare twoderivatives of Hu-Asp2(a) or Hu-Asp(b) that delete the C-terminaltransmembrane domain (SEQ ID Nos. 29-30 and 50-51, respectively) ordelete the transmembrane domain and introduce a hexa-histidine tag atthe C-terminus (SEQ ID Nos. 31-32 and 52-53) respectively, were alsoengineered using PCR. The same 5′-sense oligonucleotide primer describedabove was paired with either a 3′-antisense primer that (1) introduced atranslation termination codon after codon 453 (SEQ ID No. 3) or (2)incorporated a hexa-histidine tag followed by a translation terminationcodon in the PCR using pcDNA3.1(hygro)/Hu-Asp-2(a) as the template. Inall cases, the PCR reactions were performed amplified for 15 cyclesusing PwoI DNA polymerase (Boehringer-Mannheim) as outlined by thesupplier. The reaction products were digested to completion with BamHIand NotI and ligated to BamHII and NotI digested baculovirus transfervector pVL1393 (Invitrogen). A portion of the ligations was used totransform competent E. coli DH5 cells followed by antibiotic selectionon LB-Amp. Plasmid DNA was prepared by standard alkaline lysis andbanding in CsCl to yield the baculovirus transfer vectorspVL1393/Asp2(a), pVL1393/Asp2(a)ΔTM and pVL1393/Asp2(a)ΔTM(His)₆.Creation of recombinant baculoviruses and infection of sf9 insect cellswas performed using standard methods.

[0315] Expression by Transfection

[0316] Transient and stable expression of Hu-Asp2(a)ΔTM andHu-Asp2(a)ΔTM(His)₆ in High 5 insect cells was performed using theinsect expression vector pIZNV5-His. The DNA inserts from the expressionplasmids vectors pVL1393/Asp2(a), pVL1393/Asp2(a)ΔTM andpVL1393/Asp2(a)ΔTM(His)₆ were excised by double digestion with BamHI andNotI and subcloned into BamHI and NotI digested pIZ/V5-His usingstandard methods. The resulting expression plasmids, referred to aspIZ/Hu-Asp2ATM and pIZ/Hu-Asp2ATM(His)₆, were prepared as describedabove.

[0317] For transfection, High 5 insect cells were cultured in High Fiveserum free medium supplemented with 10 [Lg/ml gentamycin at 27° C. insealed flasks. Transfections were performed using High five cells, Highfive serum free media supplemented with 10 μg/ml gentamycin, andInsectinPlus liposomes (Invitrogen, Carlsbad, Calif.) using standardmethods.

[0318] For large scale transient transfections, 1.2×10⁷ high five cellswere plated in a 150 mm tissue culture dish and allowed to attach atroom temperature for 15-30 minutes. During the attachment time theDNA/liposome mixture was prepared by mixing 6 ml of serum free media, 60μg Hu-Asp2(a)ΔTM/pIZ (+/−His) DNA and 120 μl of Insectin Plus andincubating at room temperature for 15 minutes. The plating media wasremoved from the dish of cells and replaced with the DNA/liposomemixture for 4 hours at room temperature with constant rocking at 2 rpm.An additional 6 ml of media was added to the dish prior to incubationfor 4 days at 27° C. in a humid incubator. Four days post transfectionthe media was harvested, clarified by centrifugation at 500× g, assayedfor Hu-Asp2(a) expression by Western blotting. For stable expression,the cells were treated with 50 μg/ml Zeocin and the surviving pool usedto prepared clonal cells by limiting dilution followed by analysis ofthe expression level as noted above.

[0319] Purification of Hu-Asp2(a)ΔTM and Hu-Asp2(a)ΔTM(His)₆

[0320] Removal of the transmembrane segment from Hu-Asp2(a) resulted inthe secretion of the polypeptide into the culture medium. Followingprotein production by either baculovirus infection or transfection, theconditioned medium was harvested, clarified by centrifugation, anddialyzed against Tris-HCl (pH 8.0). This material was then purified bysuccessive chromatography by anion exchange (Tris-HCl, pH 8.0) followedby cation exchange chromatography (Acetate buffer at pH 4.5) using NaClgradients. The elution profile was monitored by (1) Western blotanalysis and (2) by activity assay using the peptide substrate describedin Example 12. For the Hu-Asp2(a)ΔTM(His)₆, the conditioned medium wasdialyzed against Tris buffer (pH 8.0) and purified by sequentialchromatography on IMAC resin followed by anion exchange chromatography.

[0321] Amino-terminal sequence analysis of the purifiedHu-Asp2(a)ΔTM(His)₆ protein revealed that the signal peptide had beencleaved [TQHGIRLPLR, corresponding to SEQ ID NO: 32, residues 22-3].

EXAMPLE 11 Expression of Hu-Asp2(a) and Hu-Asp(b) in CHO cells

[0322] The materials (vectors, host cells, etc.) and methods describedherein for expression of Hu-Asp2(a) are intended to be equallyapplicable for expression of Hu-Asp2(b).

[0323] Heterologous Expression of Hu-Asp-2(a) in CHO-K] Cells

[0324] The entire coding sequence of Hu-Asp2(a) was cloned into themammalian expression vector pcDNA3.1 (+)Hygro (Invitrogen, Carlsbad,Calif.) which contains the CMV immediate early promoter and bGHpolyadenylation signal to drive over expression. The expression plasmid,pcDNA3.1(+)Hygro/Hu-Asp2(a), was prepared by alkaline lysis and bandingin CsCl and completely sequenced on both strands to verify the integrityof the coding sequence.

[0325] Wild-type Chinese hamster ovary cells (CHO-K1) were obtained fromthe ATCC. The cells were maintained in monolayer cultures in A-MEMcontaining 10% FCS at 37° C. in 5% CO₂. Two 100 mm dishes of CHO-K1cells (60% confluent) were transfected with pcDNA3.1 (+)/Hygro alone(mock) or pcDNA3.1 (+)Hygro/Hu-Asp2(a) or pcDNA3. 1 (+)Hygro/Hu-Asp2(b)using the cationic liposome DOTAP as recommended by the supplier (Roche,Indianapolis, Ind.). The cells were treated with the plasmidDNA/liposome mixtures for 15 hours and then the medium replaced withgrowth medium containing 500 Units/ml hygromycin B. In the case ofpcDNA3.1(+)Hygro/Hu-Asp2(a) or (b) transfected CHO-Klcells, individualhygromycin B-resistant cells were cloned by limiting dilution. Followingclonal expansion of the individual cell lines, expression of Hu-Asp2(a)or Hu-Asp2(b) protein was assessed by Western blot analysis using apolyclonal rabbit antiserum raised against recombinant Hu-Asp2 preparedby expression in E. coli. Near confluent dishes of each cell line wereharvested by scraping into PBS and the cells recovered bycentrifugation. The cell pellets were resuspended in cold lysis buffer(25 mM Tris-HCl (pH 8.0)/5 mM EDTA) containing protease inhibitors andthe cells lysed by sonication. The soluble and membrane fractions wereseparated by centrifugation (105,000×g, 60 min) and normalized amountsof protein from each fraction were then separated by SDS-PAGE. Followingelectrotransfer of the separated polypeptides to PVDF membranes,Hu-Asp-2(a) or Hu-Asp2(b) protein was detected using rabbit anti-Hu-Asp2antiserum (1/1000 dilution) and the antibody-antigen complexes werevisualized using alkaline phosphatase conjugated goat anti-rabbitantibodies (1/2500). A specific immunoreactive protein with an apparentMr value of 65 kDa was detected in pcDNA3.1 (+)Hygro/Hu-Asp2 transfectedcells and not mock-transfected cells. Also, the Hu-Asp2 polypeptide wasonly detected in the membrane fraction, consistent with the presence ofa signal peptide and single transmembrane domain in the predictedsequence. Based on this analysis, clone #5 had the highest expressionlevel of Hu-Asp2(a) protein and this production cell lines was scaled upto provide material for purification.

[0326] Purification of Recombinant Hu-Asp-2(a) from CHO-KI/Hu-Asp2 Clone#5

[0327] In a typical purification, clone #5 cell pellets derived from 20150 mm dishes of confluent cells, were used as the starting material.The cell pellets were resuspended in 50 ml cold lysis buffer asdescribed above. The cells were lysed by polytron homogenization (2×20sec) and the lysate centrifuged at 338,000×g for 20 minutes. Themembrane pellet was then resuspended in 20 ml of cold lysis buffercontaining 50 mM P-octylglucoside followed by rocking at 4° C. for 1hour. The detergent extract was clarified by centrifugation at 338,000×gfor 20 minutes and the supernatant taken for further analysis.

[0328] The β-octylglucoside extract was applied to a Mono Q anionexchange column that was previously equilibrated with 25 mM Tris-HCl (pH8.0)/50 mM P-octylglucoside. Following sample application, the columnwas eluted with a linear gradient of increasing NaCl concentration(0-1.0 M over 30 minutes) and individual fractions assayed by Westernblot analysis and for β-secretase activity (see below). Fractionscontaining both Hu-Asp-2(a) immunoreactivity and β-secretase activitywere pooled and dialyzed against 25 mM NaOAc (pH 4.5)/50 mMp-octylglucoside. Following dialysis, precipitated material was removedby centrifugation and the soluble material chromatographed on a MonoScation exchange column that was previously equilibrated in 25 mM NaOAc(pH 4.5)/50 mM β-octylglucoside. The column was eluted using a lineargradient of increasing NaCl concentration (0-1.0 M over 30 minutes) andindividual fractions assayed by Western blot analysis and forβ-secretase activity. Fractions containing both Hu-Asp2 immunoreactivityand β-secretase activity were combined and determined to be >95% pure bySDS-PAGE/Coomassie Blue staining.

[0329] The same methods were used to express and purify Hu-Asp2(b).

EXAMPLE 12 Assay of Hu-Asp2 β-Secretase Activity using PeptideSubstrates

[0330] β-Secretase Assay

[0331] Recombinant human Asp2(a) prepared in CHO cells and purified asdescribed in Example 11 was used to assay Asp2(a) proteolytic activitydirectly. Activity assays for Asp2(a) were performed using syntheticpeptide substrates containing either the wild-type APP β-secretase site(SEVKM↓DAEFR; SEQ ID NO: 64), the Swedish KM→NL mutation (SEVNL↓DAEFR;SEQ ID NO: 63), or the Aβ40 and 42 γ-secretase sites (RRGGVV↓IA↓TVIVGER;SEQ ID NO: 65). Reactions were performed in 50 mM2-[N-morpholino]ethane-sulfonate (“Na-MES,” pH 5.5) containing 1%β-octylglucoside, 70 mM peptide substrate, and recombinant Asp2(a) (1-5μg protein) for various times at 37° C. The reaction products werequantified by RP-HPLC using a linear gradient from 0-70 B over 30minutes (A=0. 1% TFA in water, B=0.1%TFA/10%water/90%AcCN). The elutionprofile was monitored by absorbance at 214 nm. In preliminaryexperiments, the two product peaks which eluted before the intactpeptide substrate, were confirmed to have the sequence DAEFR (SEQ ID NO:72)and SEVNL (SEQ ID NO: 73) using both Edman sequencing and MADLI-TOFmass spectrometry. Percent hydrolysis of the peptide substrate wascalculated by comparing the integrated peak areas for the two productpeptides and the starting material derived from the absorbance at 214nm. The sequence of cleavage/hydrolysis products was confirmed usingEdman sequencing and MADLI-TOF mass spectrometry.

[0332] The behavior of purified Asp2(a) in the proteolysis assays wasconsistent with the prior anti-sense studies which indicated thatAsp2(a) possesses β-secretase activity. Maximal proteolysis was seenwith the Swedigh β-secretase peptide, which, after 6 hours, was about10-fold higher than wild type APP.

[0333] The specificity of the protease cleavage reaction was determinedby performing the β-secretase assay in the presence of 8 μM pepstatin Aand the presence of a cocktail of protease inhibitors (10 μM leupeptin,10 μM E64, and 5 mM EDTA). Proteolytic activity was insensitive to boththe pepstatin and the cocktail, which are inhibitors of cathepsin D (andother aspartyl proteases), serine proteases, cysteinyl proteases, andmetalloproteases, respectively.

[0334] Hu-Asp2(b) when similarly expressed in CHO cells and purifiedusing identical conditions for extraction with β-octylglucoside andsequential chromatography over Mono Q and Mono S also cleaves theSwedish β-secretase peptide in proteolysis assays using identical assayconditions.

[0335] Collectively, this data establishes that both forms of Asp2(Hu-Asp2(a) and Hu-Asp2(b)) act directly in cell-free assays to cleavesynthetic APP peptides at the β-secretase site, and that the rate ofcleavage is greatly increased by the Swedish KM→NL mutation that isassociated with Alzheimer's disease.

[0336] An alternative β-secretase assay utilizes internally quenchedfluorescent substrates to monitor enzyme activity using fluorescencespectroscopy in a single sample or multiwell format. Each reactioncontained 50 mM Na-MES (pH 5.5), peptide substrate MCA-EVKMDAEF[K-DNP](SEQ ID NO: 71; BioSource International) (50 μM) and purified Hu-Asp-2enzyme. These components were equilibrated to 37° C. for various timesand the reaction initiated by addition of substrate. Excitation wasperformed at 330 nm and the reaction kinetics were monitored bymeasuring the fluorescence emission at 390 nm. To detect compounds thatmodulate Hu-Asp-2 activity, the test compounds were added during thepreincubation phase of the reaction and the kinetics of the reactionmonitored as described above. Activators are scored as compounds thatincrease the rate of appearance of fluorescence while inhibitorsdecrease the rate of appearance of fluorescence.

[0337] It will be clear that the invention may be practiced otherwisethan as particularly described in the foregoing description andexamples.

[0338] Numerous modifications and variations of the present inventionare possible in light of the above teachings and, therefore, are withinthe scope of the invention. The entire disclosure of all publicationscited herein are hereby incorporated by reference.

What is claimed is:
 1. A purified polynucleotide comprising a nucleotidesequence encoding a polypeptide that comprises a fragment of a mammalianAsp2 protein, wherein said polypeptide lacks the Asp2 transmembranedomain of said Asp2 protein, and wherein the polypeptide and thefragment retain β-secretase activity of said Asp2 protein.
 2. Apolynulcleotide of claim 2 wherein the polypeptide comprises a fragmentof human Asp2 protein.
 3. A polynucleotide of claim 2 wherein thepolypeptide comprises a fragment of Asp2(a) having the amino acidsequence set forth as SEQ ID NO: 4, and wherein the polypeptide lacksthe transmembrane domain amino acids 455-477 of SEQ ID NO:
 4. 4. Apolynucleotide of claim 3 , wherein the polypeptide further lackscytoplasmic domain amino acids 478-501 of SEQ ID NO:
 4. 5. A purifiedpolynucleotide of claim 4 , wherein said polypeptide further lacks aminoacids 420-454 of SEQ ID NO:
 4. 6. A polynucleotide of claim 3 , whereinthe polypeptide comprises an amino acid sequence: that includes aminoacids 58-419 of SEQ ID NO: 4, and that lacks amino acids 22-57 of SEQ IDNO:
 4. 7. A polynucleotide of claim 3 , wherein the polypeptidecomprises an amino acid sequence: that includes amino acids 46-419 ofSEQ ID NO: 4, and that lacks amino acids 22-45 of SEQ ID NO:
 4. 8. Apolynucleotide of claim 3 , wherein the polypeptide comprises an aminoacid sequence that includes amino acids 22-454 of SEQ ID NO:
 4. 9. Apolynucleotide of claim 2 , wherein the polypeptide comprises a fragmentof human Asp2(b) having the amino acid set forth in SEQ ID NO: 6, andwherein the polypeptide lacks transmembrane domain amino acids 430-452of SEQ ID NO:
 6. 10. A polynucleotide of claim 9 , wherein thepolypeptide lacks cytoplasmic domain amino acids 453-476 of SEQ ID NO:6.
 11. A polynucleotide of claim 10 , wherein the polypeptide furtherlacks amino acids 395-429 of SEQ ID NO:
 6. 12. A polynucleotide of claim9 , wherein the polypeptide comprises an amino acid sequence: thatincludes amino acids 58-394 of SEQ ID NO: 6, and that lacks amino acids22 to 57 of SEQ ID NO:
 6. 13. A polynucleotide of claim 10 , wherein thepolypeptide comprises an amino acid sequence: that includes amino acids46-394 of SEQ ID NO: 6, and that lacks amino acids 22-45 of SEQ ID NO:6.
 14. A polynucleotide of claim 9 , wherein the polypeptide comprisesan amino acid sequence that includes amino acids 22 to 429 of SEQ ID NO:6.
 15. A vector comprising a polynucleotide of claim 1 .
 16. A host celltransformed or transfected with a vector of claim 15 .
 17. A host celltransformed or transfected with a polynucleotide of claim 1 .
 18. Apolynucleotide comprising a nucleotide sequence that hybridizes understringent conditions to a nucleic acid comprising the sequence set forthin SEQ ID NO: 4 or SEQ ID NO: 6, wherein the nucleotide sequence encodesa polypeptide having β-secretase biological activity.
 19. A vectorcomprising a polynucleotide of claim 18 .
 20. A host cell transformed ortransfected with a polynucleotide of claim 19 .
 21. A vector comprisinga polynucleotide of claim 3 .
 22. A host cell transformed or transfectedwith a vector of claim 21 .
 23. A vector comprising a polynucleotide ofclaim 4 .
 24. A host cell transformed or transfected with a vector ofclaim 23 .
 25. A vector comprising a polynucleotide of claim 5 .
 26. Ahost cell transformed or transfected with a vector of claim 25 .
 27. Avector comprising a polynucleotide of claim 6 .
 28. A host celltransformed or transfected with a vector of claim 27 .
 29. A vectorcomprising a polynucleotide of claim 7 .
 30. A host cell transformed ortransfected with a vector of claim 29 .
 31. A vector comprising apolynucleotide of claim 8 .
 32. A host cell transformed or transfectedwith a vector of claim 31 .
 33. A vector comprising a polynucleotide ofclaim 9 .
 34. A host cell transformed or transfected with a vector ofclaim 33 .
 35. A vector comprising a polynucleotide of claim 10 .
 36. Ahost cell transformned or transfected with a vector of claim 35 .
 37. Avector comprising a polynucleotide of claim 11 .
 38. A host celltransformed or transfected with a vector of claim 37 .
 39. A vectorcomprising a polynucleotide of claim 12 .
 40. A host cell transformed ortransfected with a vector of claim 39 .
 41. A vector comprising apolynucleotide of claim 13 .
 42. A host cell transformed or transfectedwith a vector of claim 41 .
 43. A vector comprising a polynucleotide ofclaim 14 .
 44. A host cell transformed or transfected with a vector ofclaim 43 .